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FirstDiscovery3.0

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1. Glide panel in Maestro Ligand folder Ligand to Define Grid panel Output folder sss 90 panel teo tacet EROS 65 POSE VIEWED eiiis 103 PoseWrite panel s 107 Reference Ligand panel mE Scoring folder sss 86 FirstDiscovery 3 0 User Manual Settings folder sss 70 Similarity folder 98 Site folder auiem 74 Glide constraints eesssess 65 69 Glide docking iva T standard precision subjobs Glide XP mode sss Glide Prime induced fit TI glide rescore utility sse 109 glide sort utility eee 93 108 GlideScore 68 86 89 binding energy model w 114 in Liaison 114 gradient criterion 164 greedy scormg iui ote tinens 67 Breen CIOSSOS Licorne rrr tr peer 152 grids COARSE qd bim ipee ioris 88 electrostatic eee i otisses 68 receptor 67 70 Smoothed treten 68 van der Waals sese 68 TOW DONG asus aae ens a eE E EES 18 H Help b tton 4 enitn 179 help option h e 35 Help panel eee een eteenises 26 179 Hide buttoti 4 eniti 3 hierarchical filters
2. s 83 Add hydrogens toolbar button 59 adding hydrogens seesse 59 algorithm conjugate gradient sss 163 energy minimization 163 Integratioti oneris 167 SHAKE RATTLE ee 160 steepest descent cece eee 164 alpha parameter in Ewald method 159 amide bond rotation sess 83 annealing ssnin aiara 68 applyhtteat scissa 2590 applyhtreat brief description 23 00 atom constraints sisisi disisi 160 ETIN 160 not used in Glide 160 OSE CE 142 160 Atom Selection dialog box ASD 21 80 131 atoms buffered vesener 131 162 frOZGD ish saei ER 131 161 harmonically restrained 162 Selecting siepe vert 21 22 AULO FEI pcs sienten redes 26 179 B backbone CUtS ir ette eren 150 backbone picking residue selection by 150 Balloon help esses 26 179 b siS S6C ii pn n oH ed 152 batch processing of ligands 110 binding affinity see 68 binding energy model Glid Score innen 114 in Liaison FirstDiscovery 3 0 User Manual bond constraints eene 160 bonds rotatable seeeeeeee 65 boundary conditions periodic 158 bounding box eere 76 box
3. sess 86 hydrogen treatment esee 59 hydrogen bond score sss 90 hydrogen bonding interaction 95 I identical chains see 43 identical sequences sss 42 Impact atom constraints sse 160 Impact bond constraints 160 impact command sees 27 29 Impact constraints eee 160 buffered atom 131 162 frozen atom eeseeeeitnoietiee 131 Impact Dynamics panel 165 Impact energy minimization 162 implicit solvent models 136 159 183 Index import structure 39 Imptet utility enitn 37 58 included entries sss 16 ind ced fitit hne os nes JT Induced Fit protocol 69 initial step size of minimization cycle 164 in place scoring 84 93 integration algorithm Il MD inicie iie soto 167 RRESPA 2 eite tien 167 Verlet s ciere 167 interface behavior of Maestro 5 internal energy esee 87 internal strain energy eene 68 ionization state expander 63 ionizer utility acoger ente 63 TONS QM region sirna 151 J Brar 139 flag Settings ue eonenetes 148 keywords 5 eret 148 para
4. sess 169 reference ligand aene 85 region boundaries QSite 147 reject pose unless eeene 89 residue selection for QM region 150 residue based cutoff distance 157 Reversible REference System Propagator Algo rithm see RRESPA rigid docking sss 66 84 93 ligands neci ttt tees 66 rigid receptor a 69 ring flips allowing we 84 ring conf brief description 61 186 IS E A ET oc eee Abi dr 65 TMS distabee usen epis 85 rotamer groups ligand 65 66 rotatable bonds sees 65 TOUS SCORC cedere emi 88 SCTECMING ieee rhe eere Pega pan 89 RRESPA integration algorithm 167 S Scale radius 1f iisotid deseen 84 Scaling of vdW radii suse TI Schr dinger contact information 180 SCHRODINGER utilities directory 93 score Coulomb van der Waals 90 hydrogen bond sess 90 in tal hgand 5 tiem 90 TOU SDs ceteri edes 88 scoring uL 89 in place i iii en ede ledio terere 93 scoring function 68 87 88 scoring in place sese 84 Scratclr entries eid ee istheeteti 12 Scratch prOJeets ue cesa secet hrs 12 screening rough score
5. 139 82 The QSite Panel a A a E EEES 140 8 3 The Potential Eolder eorr eee aE E a aee e Leap a ERE EUH e E 140 8 4 The Constraints Folder s icsccisestevsdsassssesgsegreosoeedareenalvsapesossbolebeseguasedenseenpeerstads 142 5 5 The Minimization Foldet ec icon tr orte rine inini 143 8 0 The Optimization Folder irit emeret eerte eiae 144 8 7 The QM Settings Folder repe teuer rie ver qat eee YER Qo da 147 8 7 1 OM Settings Folder Peatufes ue e rete ettet dhs ees denne 147 8 7 2 The QM Residues Ligands Panel rmt 149 8 7 3 The QM Region lons Panel 2 eee tate et een 151 Chapter 9 Energy Minimization eese eee eere eee esteso en senno n sense ene s tasto 153 9 I Basic Impact Applications sereine recette bee Pr Ren RE Rd Un 153 92 Using the Bnergy Minimization Panel ettet rnnt m 153 9 3 Energy Minimization Panel Peat tes eee rtr ep entere nee Stan ie nan 154 9 4 The Potential Foldet suerte EE ente teet teen Sea etate raa a Duae carae in ee TEE 154 94 1 Potential Folder Opts isc iieri trot reete terrere 154 9 4 2 Potential Folder Methods sese 156 0 4 3 The Truncation Panel arccos eter tetro sto etn orte dn 157 9 4 4 The Fast Multipol Method Panel 5 tme 157 9 4 5 The Periodic Boundary Conditions Panel usse 158 9 4 6 The Continuum Solvation Panel esee 159
6. 13 subjobs Glide docking 110 subset test Glide sss 66 summation method Ewald 159 Surface Generalized Bohr SGB 140 Surface Generalized Born SGB 113 159 symmetry equivalent atoms 95 T tautomerizer brief description 61 Technical Notes sse 68 technical support seese 26 179 Inbrgp C 39 Build patel tite 20 main window 8 11 Project Table panel 14 trajectory analysis eese 169 trajectory file ocn 169 analysis niece eriiasdtes 28 transition state optimization LSD sie etiem iret 146 d 146 Standard ees 146 trigonal nitrogen centers eese 83 Truncated Newton TN algorithm 163 164 Truncated Newton minimization 143 FirstDiscovery 3 0 User Manual Index truncation nonbonded interactions 141 156 protein complex structure 42 U undoing Maestro operations 24 Use Smoothing esee 158 utilities Command line eeeeeese 35 PIE r score iie ieri toreie 109 glide SOT eem 93 108 help option h sess 35 Jinptet si eie tries 37 58 JODIZGE tici de EA Aie 63 para glide 32 65
7. Option Description WAIT Keep the Impact process in the foreground instead of returning a command prompt Does not return until job completes This is useful in command scripts in which you have specified actions to take only after the Impact job finishes Without this switch the Impact job is automatically backgrounded WHICH This switch is a diagnostic tool printing the available Impact installa tions you can use for the local machine The job itself is not submit ted The first one listed is the default path the options REL VER and ARCH can direct your job to use a different installation REL release This option selects a specific version number of Impact to use The default is the latest highest number Formats like REL v3 0 REL 10003 and REL 27 are supported VER pattern If you have multiple installations installed you can specify a pattern with the VER option that matches the installation path to use for your job The default installation is the one printed by WHICH ARCH platform If you have more than one architecture installed for a given system e g AIX com and AIX pwr3 then this flag can be used to select either of them such as ARCH pwr3 LOCAL Force remote jobs to run in a local directory rather than on the remote host Only active when HOST is used 3 4 Running Jobs From the Command Line The SCHRODINGER environment variable must be set for Maestro to load and sta
8. Index OPES AA cete orm 67 68 154 overview of protein preparation 38 P para glide utility 32 65 82 110 parallel processing esse 33 and continuum solvation 148 Jaguar eere 148 OSE Losssocponmietememd ien 141 See also distributed processing parameter file molecular mechanics 154 periodic boundary conditions 140 156 158 165 ICE States coco enorme ren 8 21 picking controls sees 80 Poisson Boltzmann Solver PBF 159 Pose Viewer See Glide pose ligand nienn rentes 65 poses per ligand maximum number initiale oet itm IRE refined potential energy pprep utility inerte 37 51 Preferences panel sss 23 24 luu 69 processors multiple sss 148 product installation sss 179 project entries ostio 12 Project Facility introduction 12 Project Table panel sss 13 MEN S oe eontr IHRE DERE teen 15 mouse functions esese 16 17 shortcut keys sseseeseeene 17 PEOJO CUS m 12 protein MUMET C 2 eie ettet 42 preparation for pprep overview 38 protein complex structure importing truncating protein preparation incorporate results as 33
9. Liaison jobs jobname min mae and or jobname fin mae files are written instead 28 FirstDiscovery 3 0 User Manual Chapter 3 FirstDiscovery from the Command Line Glide jobs Glide writes intermediate Maestro format structure output to job name_raw mae files which are incremented Table 3 1 contains descriptions of the various file types For more information see the Maestro online he Ip or the FirstDiscovery Command Reference Manual Table 3 1 FirstDiscovery File Extensions Extension Description inp Impact input file or script Impact input files are formatted plain text files written in the Impact input file language DICE Maestro creates Impact input files before job submission or you can create or edit them manually with a text editor mae A Maestro format structure file a plain text file written by Maestro contain ing atom bond and other information for one or more molecules log An Impact log file If specified a Log file captures standard output and jaguar in ODE 01 02 etc out mae raw mae standard error messages in text form This file is overwritten during subse quent runs The Jaguar input file for a QSite calculation An Impact output file containing information similar to that found in log files no standard error Output files are appended with numerical extensions when the input file is run again Up to 99 output files are retained A file containing res
10. Q E 44 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation 4 7 Adjusting the Protein Metal Ions and Cofactors 4 7 Proteins That Already Include Hydrogen Atoms If the protein already includes hydrogen atoms you will need to decide how to proceed If all hydrogens are present you could use the structure as is and omit running the protein preparation procedure This approach is not recommended unless you are absolutely satis fied that the structure is properly prepared and contains no untenable steric clashes Other wise follow the steps provided below to continue the preparation procedure 4 7 2 Checking the Protein Structure for Metal Ions and Cofactors Ensure that the protein with metals and cofactors is included in the Workspace 2 To help find any metal ions or cofactors recolor the atoms by element On the toolbar choose Element from the Color all atoms by scheme button menu D All atoms in the Workspace are now colored by element 3 Examine the protein structure to determine how to continue If the protein contains neither metal ions nor cofactors proceed to Section 4 8 If the protein contains metal ions but no cofactors continue with Section 4 7 3 and check metal ion properties before proceeding to Section 4 8 Ifthe protein contains cofactors but no metal ions continue with Sections 4 7 4 and 4 7 5 and check cofactor properties before proceeding to Section 4 8 If the prote
11. 6 11 2 glide rescore Purpose Replaces the docking score properties in Glide pose output files with different values so that the glide sort best by title option can be used to combine different screens See Section 6 11 1 Syntax SSCHRODINGER utilities glide rescore options pv or lib files Options rank Replace docking score with ligand rank default mode offset value Replace docking score with GlideScore plus this offset average Calculate the average GlideScore over all the poses no output besides this average is produced top number Average only the top number poses every number Print running averages every multiple of number poses o output file Output to this file name instead of default name input file rank mae or input file offset mae FirstDiscovery 3 0 User Manual 109 Chapter 6 Glide h Print help message and quit v Print version number and quit Only one of rank offset and average can be used at a time If none is specified rank is assumed Using top and or every implies average mode 6 11 3 para glide Purpose Submits batches of ligand structures to multiple processors for Glide docking jobs Syntax SSCHRODINGER utilities para glide i inp file options Options n njobs Number of subjobs to prepare f firstlig First ligand to include 1 lastlig Last ligand to include j jobnum Subjob number to prepare X Launch jobs after writin
12. FirstDiscovery 3 0 User Manual 25 Chapter 2 Introduction to Maestro 2 11 Getting Help Maestro comes with automatic context sensitive help Auto Help Balloon help tool tips an online help facility and a user manual To get help follow the steps below Check the Auto Help text box below the title bar of the main window If help is avail able for the task you are performing it is automatically displayed there It describes what actions are needed to perform the task If your question concerns a GUI element such as a button or option there may be Balloon help for the item Pause the cursor over the element If the Balloon help does not appear check that Show Balloon Help is selected in the Help menu of the main window If there is Balloon help for the element it appears within a few seconds If you do not find the help you need using either of the steps above click the Help button in the lower right corner of the appropriate panel The Help panel is displayed with a relevant help topic For help with a concept or action not associated with a panel open the Help panel from the Help menu or press ALT H If you do not find the information you need in the Maestro help system check the following sources The Maestro User Manual The Maestro Release Notes The Frequently Asked Questions page found at http www schrodinger com Support fag html 2 12 Ending a Maestro Session To end a Maestro session choose Quit from t
13. FirstDiscovery provides command line utilities and applications to aid in structure prepa ration structure file format conversion and structure database handling The Glide module has its own set of utilities The command line utilities glide sort glide rescore and para_glide are summarized in this section FirstDiscovery 3 0 User Manual 107 Chapter 6 Glide 6 11 1 glide sort Purpose Re ranks Glide poses by custom criteria or combines job outputs into one file Syntax S SCHRODINGER utilities glide sort mode options Glide pose files Modes of Operation At least one of these options is required o output file r report file gt R Sorting Options use_dscore use gscore use cvdw use emodel nosort Output Options n nreport norecep best best by lignum best by title h V 108 Write the best scoring poses to output file Create a report of the best scores in report file Write a report of the best scores to standard output Default Sort poses based on the docking score in Glide output poses Docking score is a placeholder for the property on which you would like to sort poses Initially it is equal to GlideScore but glide rescore can be used to replace it with other values see Section 6 11 2 Sort poses based on GlideScore Overrides use of docking score field Sort poses based on Coulomb van der Waals energy E CvdW Overrides use of docking scor
14. This text box specifies the value of the dielectric constant used in the electrostatic calcu lations 9 4 2 Potential Folder Methods The lower part of the Potential folder allows you to choose among molecular mechanics treatments When the check box for a method is selected clicking the associated Settings button opens a panel of relevant options The methods are listed briefly in this section and then each Settings panel is described in more detail Use truncation In molecular mechanics calculations it is often impractical to include the nonbonded electrostatic and van der Waals interactions between every pair of atoms For large systems many such pairs are separated by a great distance and contribute little to the overall interaction energy Judicious use of truncation to remove interactions between widely separated pairs of atoms is an important strategy for reducing the time and memory required to perform calculations on large systems Use fast multipole method The Fast Multipole Method FMM is an algorithm for speeding up the electrostatic part of the molecular mechanics calculation for large systems Use periodic boundary conditions Periodic boundary conditions are commonly used for calculations with explicit solvent but can be employed for any periodic system Use continuum solvation Two implicit solvent models the Surface Generalized Born Model SGB and the Poisson Boltzmann Solver PBF are available in Im
15. W Show jobs from current project only fhome saunders Documentation FirstDisco Figure 2 7 The Monitor panel Maestro also has a job control panel for monitoring the progress of jobs and for pausing resuming or killing jobs the Monitor panel All jobs that belong to your user ID can be displayed in the Monitor panel whether or not they were started from Maestro The text pane shows some kinds of output from the job that is being monitored such as the contents of the log file The Monitor panel opens automatically when you start a job If it is not open you can open it by choosing Monitor from the Applications menu in the Maestro main window While jobs are running the Detach Pause Resume Stop Kill and Update buttons are active When there are no jobs currently running only the Monitor and Delete buttons are active These buttons act on the selected job By default only jobs started from the current project are shown To show other jobs deselect Show jobs from current project only When a job that is being monitored ends the results are automatically incorporated into the project If a job that is not currently being monitored ends you can select it in the Monitor panel and incorporate the results Monitored jobs are incorporated only if they are part of the project You can monitor jobs that are not part of the project but their results are not incorporated To add their results to the project you must import them
16. neighbors that are not close 2 Slow Long distance nonbonded 1 All text boxes have acceptable ranges of any integer value greater than one These entries modify the time step for the underlying MD or HMC simulation in the fol lowing way Suppose that the global Time step specified in the Dynamics folder of the Impact Dynamics panel or the Hybrid MC folder of the Impact Hybrid Monte Carlo panel is 6 Then the time step used to integrate the slow forces is 6 1 while the time step for medium forces is 6 1 x 2 and that for fast forces is 6 1 x 2 x 4 Thus the integration time step decreases as the product of the cumulative RRESPA update frequencies in going from slow to fast forces When FMM is not used this is the more common case only the Fast forces text box affects the calculation In this case the Medium and Slow forces are combined and use the global Time step set in the Dynamics folder of the Impact Dynamics Impact Dynamics idynamics lei Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries lt gt Replacing existing entries lt gt Do not incorporate Potential Constraints MD Parameters Dynamics Integration algorithm RRESPA RRESPA update frequencies Fast forces 4 Medium forces 2 Slow forces 1 W Stop overall motion Frequency of printing information 5 J Collect MD stati
17. sess 27 3 1 4 Force Fields and Write Template sese 28 3 2 Pile Name C onyentiOnS 4 eee ete rr reso e re Ee ER a RR ERE EROR erre eee EOS 28 3 3 The Impact Command Usage Summary esee ettet tnnt itin 20 3 4 Running Jobs From the Command Line eene 31 3 4 1 Protein Preparation snoin aerianas a Ce er ERES Ee BEES 32 BAD Gld iue tas tte tme eti ee dte aisles 32 EX Nri m 33 cm EQ 33 341 5 Basic Impact p eet nea ER PEN E ERE RU Rr HU SHE UE e REP EER 34 3 4 6 Using Job Control Commands essen 34 3 5 Using Command Line Utilities iiem retener eere rere iaoe 35 Chapter 4 Protein Preparation 4 eerie esee eee eese e enses tns tn stas n senatu sena 37 4 1 Protein and Ligand Structure Preparation eee 37 42 The ProtemPrep Panel entier tret terrere ete RE ede 37 4 5 St ep Dy Step OVERVIEW actae teret re rer trn REUS ESSE EERERERE Capote Pee REPRE ERR 38 4 4 Importing the Protein Complex Structure 39 4 5 Deleting Unwanted Waters scccccevsssccsvecesscdsecbevccsieevsdedsadseeveeg soceavtavbeseoeea retten 39 4 5 1 Locating Structural Waters te s asini Dresser eher RE eise E 40 4 5 2 Should Structural Waters Be Kept essere 41 4 5 3 Deleting All Water Molecules seeseeseeeeeeeeeeeennneennne 41 4 5 4 Deleting Distant Water
18. Ligand button becomes available Click it to open the Ligand to Define Grid panel described in Section 6 4 2 The ligand centroid is computed as half the sum of the smallest and largest x y and z coordinates of any atom The Active site residues option centers the box at the centroid of a set of active site residues When this option is set the Specify Active Site Residues button becomes available Click it to open the Specify Active Site Residues panel described in Section 6 4 3 The Supplied X Y Z coordinates option allows you to set the center of the enclosing box directly by typing the coordinates into the X Y and Z text boxes Even if this option is not selected the values in the X Y and Z text fields are updated to show the current box center defined by the selected option The enclosing box can be reposi tioned by entering new centering values into the X Y and Z text boxes To provide visual guidance the X Y and Z coordinate axes are displayed at the center of the ligand bounding box Size of bounding box for placing ligand center The up and down arrows increase and decrease the size of the bounding box The bounding box is the region within the enclosing box within which Glide may place the ligand center The size of the bounding box can be set to between 6 and 30 on each side in increments of 2 If the bounding box is currently displayed in the Workspace it is redrawn as the box size is changed The default l
19. OVeE VIEW s scidieeite iiie lies 38 protein preparation facility 37 protein structure multimer 38 185 Index protprep command line application 55 pyramidalization seen 83 Q OMrCODptIODS odit oer at 148 OM potential energy eene 140 OM Pegi OM iss iier hee 142 160 TOMS ceteri FREE 151 OM MM iecit ATE 139 QM MM boundary ee 150 QSite atom constraints usss 142 160 continuum solvation 141 148 CUS eR 147 description iaceret citri 140 force Meld arenaene 140 Minimization folder 143 parallel processing 141 QM Region Ions panel 151 QM Residues Ligands panel 149 QM Settings folder 147 OSite panel n nest 140 single point energy eee 145 unavailable methods 140 Quadratic Synchronous Transit QST 146 quantum mechanical calculations 139 quasi Newton method 146 quitting Maestro esee 26 R range of ligand structures 83 range value iecit eter ttn 83 raw unsorted pose file ssse 92 receptor constraint Sit S eee eects 69 receptor grids oo eee eeeeeteeeeeeeeee 67 70 Record Trajectory
20. The FirstDiscovery Command Reference Manual which contains syntax and key words for Impact command input files Starting with FirstDiscovery 3 0 the Command Reference Manual is no longer printed as hardcopy and bound with the other FirstDiscovery manuals Like other FirstDiscovery documentation it is still provided in PDF format compressed into a tar file on the FirstDiscovery CD and is available at Schr dinger s support web page http www schrodinger com Support pdf html The Maestro User Manual which describes how to use the features of Maestro including the Atom Selection Dialog ASD An appendix describes command line utilities many of which are used in FirstDiscovery The Maestro Command Reference Manual which contains commands options and arguments for running Maestro from the command line including the Atom Specifi cation Language ASL and the Entry Specification Language ESL FirstDiscovery 3 0 User Manual 1 Chapter 1 Introduction 1 1 Document Conventions In addition to the normal use of italics for names of documents the font conventions that are used in this manual are summarized in Table 1 1 Table 1 1 Font Conventions Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons labels Monospace SSCHRODINGER maestro File names directory names commands and environment variables Italics filename Text that the user must replace w
21. The QSite panel Constraints folder can be used to specify frozen atom constraints on atoms in both the QM and the MM regions but buffered atom constraints are applied only in the MM region The Liaison panel Constraints folder allows atom constraints to be applied to Liaison simulations See Section 7 8 on page 130 Note The Constraints folder in the Glide panel is used to set up Glide constraints required interactions between ligand and receptor atoms only Impact atom constraints are not used in Glide 9 5 1 Constraints Folder Features The options that are not available for Impact Energy Minimization and therefore not in the Constraints folder when it is opened from the Energy Minimization panel are described in Chapter 10 160 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization Impact Energy Minimization imini Silex Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace gt Selected entry Incorporate output into project by Appending new entries Replacing existing entries lt gt Do not incorporate Potential Constraints Minimization Frozen Atoms Buffered Atoms Start Write Job Files Hide Help Figure 9 2 The Constraints folder of the Impact Energy Minimization panel Frozen Atoms Impact calculations can be performed with some atoms completely frozen so that they never move from their initial positions during minimiza
22. The manuals and the release notes are available in PDF format from the Schr dinger web site at http www schrodinger com Support pdf html Information on additions and corrections to the manuals is also available from this web page FirstDiscovery 3 0 User Manual 179 Chapter 13 Getting Help If you have questions that have not been answered from the above sources contact Schr dinger using the information below Schr dinger E mail help schrodinger com USPS 1500 SW First Ave Suite 1180 Portland OR 97201 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Generally e mail correspondence is best because you can send machine output if neces sary When sending e mail messages please include the following information most of which can be obtained by entering SCHRODINGER machid at a command prompt All relevant user input and machine output FirstDiscovery purchaser company research institution or individual Primary FirstDiscovery user Computer platform type Operating system with version number FirstDiscovery version number Maestro version number mmshare version number 180 FirstDiscovery 3 0 User Manual Index Numerics 3D ligand structures sess 5 and 6 membered rings A active site metalin eee tertii 72 with metal atoms esses 69 acyclic torsion bonds
23. 42 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation If the binding interaction of interest takes place within a single subunit you should retain only the one ligand receptor subunit to prepare for Glide Liaison or QSite However if two identical chains are both required to form the active site neither should be deleted To see whether two duplicate chains are involved with the active site undisplay the protein s amino acid residues 1 On the toolbar choose Protein Backbone from the Undisplay button menu zi E 2 Repeat the process and choose Protein Side Chains Ligands cofactors metal ions and water molecule oxygens remain visible If two or more identical ligands or ligand cofactor groups are present then the complex is most likely a multimer and the redundant groups and the duplicate chains associated with them can be deleted 4 6 2 Retaining Needed Subunits If the protein complex structure is a multimer with duplicate binding sites it can be trun cated by deleting all but a single ligand binding site and the associated receptor subunit s If you choose not to truncate the structure skip to Section 4 7 on page 45 To remove redundant subunits or receptor sites of a multimer 1 Delete all but one ligand or ligand cofactor pairing a On the toolbar choose Molecules from the Delete button menu X b Click on any atom in a molecule to delete that molecule 2 Display the ligand or ligand cofactor pair in C
24. E Filename of Sand bindini energies i Start Write Job Files Figure 7 6 The Analysis folder of the Liaison panel Predict This option uses values of the selected binding energy model s parameters together with data retrieved from completed Liaison receptor ligand simulations to predict the binding energy for a ligand or a series of ligands The ligand names can be entered directly or can be taken from an external file The file format is described under the File Name of Ligand Names feature Binding energy model Use these options to specify which binding energy equation to use for fitting and predic tions The two choices are LIA equation This model has three parameters van der Waals o electrostatic B and cavity y as described in Section 7 1 on page 113 FirstDiscovery 3 0 User Manual 133 Chapter 7 Liaison GlideScore This is a linear model relating experimental binding energies to the GlideScore The GlideScore equation given on page 114 therefore has Slope a and Intercept b fitting parameters Fitting Parameters Prediction Parameters These text boxes allow the user to set the coefficients for the selected Binding Energy Model equation that Maestro will use in a Predict calculation For the LIA Equation these are the coefficients of the van der Waals Electrostatic and Cavity energy terms For the GlideScore model they are the Slope and Intercept coefficients These values are
25. bounding eroinin 76 CM CLOSING ranon a 75 76 buffer force setting sees 162 buffered atoms eessessss 131 162 buffered atom constraints 142 160 QNI APTE 142 160 Build panel 2 cette ee 19 building structures 18 20 button MeNi sessirnir irte 8 C Cartesian coordinate constraints 142 center of ligand eter 76 centroid ligand esses 76 CHEMS COME aint oen 68 86 close contacts eeeessssseseeeeeee 69 77 Suis em 90 COafSe grid a teer 88 Collect MD Statistics ssusss 169 command line running jobs from 31 Command Script Editor panel 23 command scripts see scripts command line application protprep 55 commands jum OD COntEOl 4 uio etras Commands Maestro text box conformational search in Glide conformations CORO eae generation in Glide FHp n scere conjugate gradient x minimization number of steps 89 constrain all bonds sssssss 160 constraints buffered atom 131 142 160 162 Cartesian 5 ne no os EGER 142 frozen atom 131 142 160 161 Glidecam ro eter 65 68 181 Index Impact 130 160 Impact bond sss 160 continuum solvation ees 156 Method Sinergi 159 OSIE ce
26. constraint essere 68 ligands Ou T 76 COMPO e 76 CiainetBr oou arto cR 66 Tlexible nie nies 66 PROG senes 150 151 nonpolar atoms eee 84 POSES M 65 protein preparation eese 49 T ferernce anos creen iie 85 residue selection 150 TAS PEE 66 structure requirements 59 ligparse brief description 61 IagPrepasicasseenenionetete die 59 63 Linear Interaction Approximation LIA 113 Linear Response Method LRM 113 Linear Synchronous Transit LST 146 list neighbor 5 aient 157 log file saving Maestro 26 long range forces in TN optimizations 164 LRM binding energy model 113 M Maestro Commands text box sesss 40 lj M 179 interface behavior sess 5 main window a6 7 menus s 7 8 quitting esit esetedeieiteeeie eitis 26 running jobs from 24 25 scratch projects sssess 12 starting 6 undoing Operations 24 working directory sss 27 FirstDiscovery 3 0 User Manual main WINDOW 0 4620 sisaesseserdeseeseuviverscecssassnierssacs 7 maximum step size of minimization cycle 164 MD Parameters folder 167 MD simulations frequency of prin
27. distance and an appropriate Z H X angle receives a score of about 0 9 kcal mol If the pose has a hydrogen bond score greater more positive than the value specified the pose is rejected The default value is 0 0 As hydrogen bond scores can only be negative use of the default value accepts all poses See Eldridge et al J Comput Aided Mol Des 1997 11 425 445 for a definition of the ChemScore Hbond term that GlideScore uses Metal ligand score lt If the pose has a metal ligand score greater than more positive or equal to this value the pose is rejected The default value is 0 0 For Glide 3 0 you should not change this value 6 7 The Output Folder The Glide Output folder organizes various options that control the final output of poses that pass successfully through Glide s various scoring stages There are two main sections to the Output folder Elimination of duplicate poses clustering Structure output 6 7 1 Elimination of Duplicate Poses Section This option ensures that poses found to be identical within the specified criteria are not replicated in the Glide output The default settings are Discard pose as duplicate if RMS distance 0 5 and maximum atomic displacement 1 3 A 90 FirstDiscovery 3 0 User Manual Chapter 6 Glide Glide glide Job dock_confgen Login saunders Host localhost 1 Settings Site Ligand Scoring output Constraints Similarity Elim
28. interpolating between them LST uses a quasi Newton method to search for the opti mum transition state geometry choosing a transition state guess structure based on the interpolation value you set using a slider The default interpolation value is 0 50 directing QSite to choose a transition state guess structure midway between reactant and product For a guess structure closer to the reactant set the interpolation value between 0 0 and 0 50 For a guess structure closer to the product set the value between 0 50 and 1 0 QST Quadratic Synchronous Transit is useful if you have initial guess structures for the reactant the product and the transition state QST uses a quasi Newton method to optimize the transition state geometry Reactant entry Product entry TS guess entry You can select the initial guess for the reactant structure by typing in the entry name from the current Project Table by clicking Choose and selecting the entry from a list or if the structure is displayed in the Workspace by selecting Pick to define entry and clicking on any atom in the structure The same options are available for selecting the Product entry and the TS guess entry 146 FirstDiscovery 3 0 User Manual Chapter 8 QSite Fraction of path between reactant and product When the TS method option menu is set to LST this slider is available By default it is 0 50 directing QSite to choose an interpolated transition state guess structure midway betw
29. residue 4 7 5 Adjusting Cofactor Atom and Bond Properties To set or change cofactor bond orders 1 If the Build panel is not displayed click Show Hide build panel on the main toolbar Z 2 On the Build panel toolbar click the Decrement bond order or Increment bond order button as appropriate Cl ec 3 Click on bonds as necessary to set the bond order FirstDiscovery 3 0 User Manual 47 Chapter 4 Protein Preparation To set or correct the formal charge on any cofactor atoms 1 On the main toolbar choose Formal Charge from the Label atoms button menu P E 2 If the Build panel is not displayed click Show Hide build panel on the main toolbar la 3 On the Build panel toolbar click on the Increment formal charge or Decrement formal charge button as appropriate XX 4 Click on an atom whose formal charge must be increased or decreased Repeat as necessary The atom labels will show the current formal charge To correct the atom type of any mistyped atoms 1 If the Build panel is not displayed click Show Hide build panel on the main toolbar Fa 2 In the Atom Properties folder of the Build panel choose Atom Type MacroModel from the Property option menu 3 Find the correct atom type for the mistyped atom and click it in the list 4 Click on the atom to be changed 5 If the cofactor contains any metal ions bonds between the metal and cofactor can be removed as in Section 4 7 3 For mo
30. 1bkm 3m 3 In this example 1bkm represents the character string entered into the Job text box and thus 1bkm is the name of the Master Liaison Run Directory The underlying ligand direc tories are 1bkm 3m 1 1bkm 3m 2 and 1lbkm 3m 3 7 2 4 Liaison Simulation Requirements The Liaison simulation requirements are A receptor structure read into Maestro before starting the job e One or more ligands If there is one ligand it can either be taken from the Workspace display or read from a file For two or more ligands a text file containing ligand names you define and the full path to the location of the ligand files on disk are required This text file can reside in any direc tory The format is LigandName space LigandLocation FirstDiscovery 3 0 User Manual 117 Chapter 7 Liaison Example Ligand1 home username LIA H01 lig mae Ligand2 home username LIA H02 lig mae Ligand3 home username LIA H03 lig mae Ligand4 home username LIA H04 lig mae Ligand5 home username LIA H05 lig mae The sampling methods available are Energy Minimization Hybrid Monte Carlo HMC Molecular Dynamics MD By far the fastest method is energy minimization Even though this method gives only a snapshot of the possible ligand receptor configurations studies to date have shown that it gives predicted binding affinities that are reasonably close to those obtained with HMC or MD Minimization is thus an attractive choice when larg
31. 2D 3D conversion if necessary The stereoizer can generate two stereoisomers per chiral center in the ligand up to a specified maximum There are three Stereoisomers options The first two options Retain specified chiralities the default and Determine chirali ties from 3D structure generate both isomers only at chiral centers where chirality is unspecified or indeterminate centers with known chirality retain that chirality The difference is that Retain specified chiralities takes its chirality data from the input file SD or Maestro while Determine chiralities from 3D structure ignores input file chiralities and takes chirality information from the 3D geometry Generate all combinations produces the maximum number of structures up to the maximum which by default is 32 stereoisomers but can be changed using Gener ate stereoisomers maximum max per ligand The ionizer following the neutralizer can generate all the ligand protonation states that would be found in the specified pH range The lonization options are Retain original state Neutralize best for QikProp Generate possible states at target pH target range This is the default and can generate several different output structures for each input structure The default pH target is 7 0 with a range of 2 0 so the default pH range is 5 0 9 0 Both the tar get and range settings can be changed Generate stereoisomers maximum max per ligand Generate low
32. 82 110 pol 37 543 esu i IS 33 V van der Waals grids sss 68 69 77 84 167 W water entry preparing eects 39 waters crystallographic esses 39 deleit misa inion ren trenes 39 in protein complex structure 39 Structural aee eet 39 working directory Maestro 27 Workspace desCEIDLOD ciii tete rennes 6 including excluding and fixing entries 16 mouse functions eeseeeee 11 Scratch Entries 12 Write Template ssi eene 28 X XP GlIde seien rore treats 65 XP iode iae eere here eterne 69 187 Index 188 FirstDiscovery 3 0 User Manual 120 West 45th Street 1500 SW First Avenue 3655 Nobel Drive Dynamostrafe 13 32nd Floor Suite 1180 Suite 430 68165 Mannheim New York NY 10036 Portland OR 97201 San Diego CA 92122 Germany SCHRODINGER
33. 9 5 Th Consttamts Folder terere ete eerte ei irae fare te aet ee oen 160 9 5 1 Constraints Folder Features erranei neesiana 160 9 5 2 The Brozen Atoms Panel sci 2255 csesesessteeacensapuidancesesaesoudaemneecsanensiers 161 9 5 3 The Buttered Atoms Panel utente tere rer 162 9 6 The Minimization Foldet issii iii ertet tete 162 FirstDiscovery 3 0 User Manual vii Contents Chapter 10 Molecular Dynamics Simulations ccccscssssscsssccesseeseseees 165 10 1 Using the Dynamics Panel tette re aieo t ee ttes 165 10 2 Dynamics Panel Feat res 2 ederet rte Ree neon 165 10 3 The Constraints Folder ebrei eec 166 10 4 The MD Parameters Folder ae ete ee age pre 167 10 5 The Dynamics Folder niet rtr aa EE EEE 170 Chapter 11 Hybrid Monte Carlo Simulations ceeeceeeeeeeees 173 11 1 Using the Hybrid Monte Carlo Panel eee 173 11 2 Impact Hybrid Monte Carlo Panel Features esee 173 11 3 The Hybrid MC Folders iret er EE eaaet EN 174 Chapter 12 Soak Add Explicit Water Solvent ceres 177 12 1 Using the Soak Panel eerte terere ete eee ettet de 177 12 2 Soak Panel Beatures ierit eerte pog tere v Ure a neg exe Hd setae 178 Chapter 13 Getting Help i cccccccsssossssesssosesasescossnossevesecsonesoes seossesseessoessvoneses 179 e M 181 viii
34. Energy Minimization Note When Use fast multipole method is selected the Truncated Newton TN minimiza tion method and the SGB continuum solvation method are unavailable To open the Fast Multipole Method panel select Use fast multipole method and click the adjacent Settings button The following options can be set Level Use this text box to set the number of levels in the hierarchical tree used in the FMM calculation This setting is relevant only when the Reversible RESPA integration propa gator is used with more than two stages See Section 10 4 on page 167 The Level parameter specifies the number of times the elementary simulation box is divided into halves along each direction a procedure known as octree decomposition Thus if Level 1 is set one division is made along X one along Y and one along Z so that the box is divided into eight sub cubes octants If Level 2 each sub cube is further divided into eight smaller cubes for a total of 64 and so on Set Level to at least 2 Larger values result in increased accuracy at the cost of longer execution time but they may be useful in very large systems Maximum Use this text box to set the maximum number of multipole moments to be used to approx imate the potential and field produced by far clusters of atoms Currently a minimum of 4 and a maximum of 20 multipoles are permitted Use smoothing If you select this option a smooth cutoff is used to separate i
35. FirstDiscovery 3 0 User Manual Chapter 1 Introduction Once you have installed FirstDiscovery according to the instructions in the Schr dinger Product Installation Guide the FirstDiscovery User Manual will help you use the First Discovery software suite Some of the material in this manual provides context and back ground information but much of it describes the options and settings needed to configure FirstDiscovery and Basic Impact applications The FirstDiscovery suite includes Glide Liaison and QSite the principal program modules Basic Impact applications Protein Preparation and supporting utilities and scripts The FirstDiscovery programs are run primarily from the Maestro graphical user interface an introduction to which appears in Chapter 2 but can also be run from the command line as described in Chapter 3 Utilities and scripts are run from the command line Both interfaces call on Impact the FirstDiscovery calculation engine For related information please see our other documentation The Schr dinger Product Installation Guide which includes installation instructions for all Schr dinger products and documentation The FirstDiscovery Quick Start Guide which contains tutorials intended to familiar ize you with protein preparation Glide Liaison and QSite The FirstDiscovery Technical Notes featuring in depth scientific discussions of Glide Liaison and QSite including performance and usage notes
36. Multiple ligands single receptor simulations only the receptor can be loaded to the Workspace The ligands are defined by specifying a file that contains the ligand names and the locations of their structure files In each case selecting certain options dims other control settings that do not apply to the options selected If the Analysis folder is active you must change the Job Type selection to Simulate in the Settings folder before opening the System folder 7 6 1 Multiple Ligands Single Receptor A multiple ligand simulation requires one receptor structure and multiple ligand struc tures The receptor structure is taken from the Workspace which must contain only this structure The control settings used to specify the ligands are described below Format of ligand files Liaison supports the three file formats listed below for reading structures from local or network mounted disks Liaison does not support Mol2 formatted files nor will it accept structures with lone pairs remove them using the Hydrogen Treatment panel select Hydrogen Treatment from the Edit menu before submitting the Liaison job Maestro Maestro written files extensions mae out or dat e MDL SD SD formatted files extensions mo1 for single structure files and sdf for multiple structure files PDB Rutgers Center for Structural Biology Protein Data Bank files extensions pdb or ent File containing a list of ligand names and associated struc
37. Run Script Command scripts cannot be used for Prime operations 22 FirstDiscovery 3 0 User Manual The Command History window displays a log of all commands issued internally within Maestro when you interact with a panel menu or structure Chapter 2 Introduction to Maestro immand Script Editor script Command History ganic Methyl nic Carbonyl Select All Deselect All Show Hide Selection T W Log commands place 1 396908 0 649130 0 000000 fragment organic Amine attach 4 fragment organic Methyl attach fragment organic Methyl attach 3 fragment organic Carbonyl attach 11 undo E E Run Script 3i ipi Expand Command Aliases Open Local Open Global Save As Hide Help Figure 2 5 The Command Script Editor panel Opens the Show Hide Command panel used to determine which commands are logged in the Command History list 2 8 Specifying a Maestro Working Directory When you use Maestro to launch FirstDiscovery jobs Maestro writes job output to the directory specified in the Directory folder of the Preferences panel By default the direc tory to which Maestro writes files the file I O directory is the directory from which you started Maestro To change this directory 1 Open the Preferences panel from the Maestro menu 2 Click the Directory tab 3 Select the option for the directory you want files to be read from and written t
38. Some operations take effect immediately such as deleting atoms Others merely define a set of atoms to be used in a subsequent task such as selecting atoms for the creation of a surface When the Atom Selection dialog box is open you cannot perform other actions except for rotation and translation of structures and picking You can also open the help viewer 2 7 Maestro Command Scripts Although you can perform nearly all Maestro supported operations through menus and panels you can also perform operations using Maestro commands or compilations of these commands called scripts Command scripts can be used to automate lengthy procedures or repetitive tasks Because all Maestro commands are logged and displayed in the Command Script Editor panel you can create a command script by performing the operations with the GUI controls copying the logged commands from the Command History list into the Script area of the panel then saving the list of copied commands as a script Short scripts can also be saved as macros which are run from the keys F1 through F12 See the Maestro User Manual for details To run an existing command script 1 Open the Command Script Editor panel from the Edit menu in the main window 2 Click Open Local and navigate to the directory containing the desired script 3 Select a script in the Files list and click Open The command script is loaded into the Script window of the Command Script Editor panel 4 Click
39. The menu is called a button menu There are two kinds of items on button menus and both kinds can be on the same menu Actions which perform an action immediately States which you set before an action is performed When you select a state it is stored and marked with a red diamond on the menu Most states on button menus are pick states see Section 2 6 on page 21 which means you must pick an atom in the Workspace before the action is performed If you click a menu button that has pick states the button is indented to indicate that picking with the selected pick state is in effect If you double click a menu button that has pick states the action is applied to all atoms Some other menu buttons support double clicking to apply an action this support is explicitly mentioned in the button description 8 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro You can show or hide the toolbar using the collapse button at the top or by selecting Toolbar from the Display menu You can hide it or move it to the right or left side of the Workspace by right clicking in the toolbar and selecting the appropriate option The buttons are described below Some descriptions refer to features not described in this chapter See the Maestro User Manual for a fuller description of these features Open a project Open the Open Project dialog box Show Hide project table Show the Project Table panel or hide it if it is displayed Crea
40. WRITE TEMPLATE while using OPLS2001 an error message appears to remind you that this command can only be used with OPLS1999 or OPLS2000 force fields To use one of these older force fields add a line to your input file before the CREATE task for example SET FFIELD OPLS1999 3 2 File Name Conventions A typical FirstDiscovery job has one command script file jobname inp one or more structure files jobname mae jobname pdb or jobname sdf and after execution several output files e g jobname out mae for structure files and jobname out for textual data If a file already has the name of an output file in many cases Impact will rename the old file with a numerical extension filename out 01 filename out 02 and so on for archival purposes The new job s output is then written to the base name filename out If you do not need the old files you can remove them Some files such as jobname 1og files are newly written each time Impact runs a calcula tion Likewise old jobname pv mae files are overwritten Other examples of files that are not incremented are jobname out mae structure files for Basic Impact minimization and QSite jobs jobname lig min mae and jobname rec min mae files for the minimization section in Liaison e jobname rec fin mae and jobname lig fin mae files for the dynamics and HMC sampling methods in Liaison In addition jobname out mae files are not produced by default for
41. a remote machine you must specify a login name for the remote machine By default the login name is set to the login name of the user who began the Maestro session If a different login name is required it must be typed here before the job is started If the Impact job is running on a local computer the Login field is ignored Host On this menu Maestro will display all hosts defined in the file SSCHRODINGER schrodinger hosts The following two options appear on the panels for QSite and for Basic Impact applica tions only Source of job input This feature is not available for Glide and Liaison jobs in which external structure data bases are commonly used When you set up other FirstDiscovery jobs you may use this feature to choose either the on screen Workspace structure or a Selected entry from the Project Table The Workspace selection is the default choice indicating that the simulation to be performed will operate on whatever atoms molecules or entries are part of the on screen structure even those atoms hidden by the Display Undisplay Atom facility Performing a simulation with Frozen or Buffered Atoms see the Constraints folder Section 9 5 on page 160 requires that you use the Workspace structure The Selected entry option is for running the simulation on whatever entry is currently selected in the Project Table irrespective of what is displayed in the Workspace Note that only one entry can be selected If more tha
42. added to the GlideScore computed in the usual way with the following ramp form Pies S lt Smin f s P nax 1 s S ain Smax E Smin Smin Ss lt Smax 0 SS The defaults are P nax 6 0 GlideScore units Smin 0 3 Smax 0 7 All three parameters are selectable in Maestro subject only to 0 0 lt Smin lt Smax lt 1 0 In particular Pmax may be negative with the effect of rewarding ligands that are dissimilar to the specified actives This is useful for finding new leads that bind well to a target but are in a different chemical family from previously known binders 6 9 2 Similarity Folder Features Grid Generation When the Glide task Set up grids is selected in the Settings folder the Generate weights option in the Similarity folder becomes available Generate weights Selecting this option makes the following features available for specifying the active and inactive compounds to be used in determining weighted similarities Filename of known actives Select a file containing the active compounds to be used in calibrating similarity weights For this purpose the file must contain at least two structures Note that a file of actives must be specified again in the docking job for both standard and weighted similarity For best results in both cases these compounds should span the range of functionality and molecule size of known actives Including multiple compounds that are closely related may be inefficien
43. backbone atom other than an alpha carbon A cut will be placed between the selected atom and the alpha carbon bonded to it 3 Pick a second backbone atom Another cut will be made between this atom and its adjacent alpha carbon and all of the backbone and side chain atoms between the two cuts will be included in the QM region A minimum of three backbone bonds must exist between any pair of backbone cuts Due to parametrization limitations back bone cuts cannot be made in glycine GLY or proline PRO residues or in residues immediately adjacent to GLY or PRO To select a side chain for inclusion in the QM region 1 Click Residue selection by sidechain picking 2 Pick any atom from the desired side chain A cut will be made between the alpha car bon and beta carbon of that residue All of the atoms in the side chain will be part of the OM region Side chain cuts can be made in any peptide residue other than alanine ALA arginine ARG glycine GLY proline PRO serine SER and threonine THR These residues are excluded because cuts for these side chains are especially difficult to parameterize The side chains for these residues can still be treated quantum mechanically using back bone cuts to select a QM region that includes the desired side chain 150 FirstDiscovery 3 0 User Manual Chapter 8 QSite Cuts in a protein ligand complex must be between atoms in peptide residues Covalently bound ligands can be included in t
44. be useful 7 7 2 Ligand Simulation and Ligand Receptor Simulation Depending on the sampling method chosen some or all of the following options are avail able in the lower section of the folder The two sub tabs affect simulations on the free ligand Ligand Simulation and bound complex Ligand Receptor Simulation respectively The selection options are Minimize before simulation This toggle is active only for Hybrid Monte Carlo and Molecular Dynamics sampling It places a minimization task MINIMIZE in the Liaison input file in front of the LRM simulation task Its purpose is to ensure that the simulated structure does not have signifi cant excess potential energy from bad internal contacts Maximum minimization steps This text box sets the maximum number of minimization steps This option is active only when Minimize before simulation is selected RMS grad for convergence This text box sets the criterion on the rms gradient for convergence of the minimization kcal mol A This option is active only when Minimize before simulation is selected Heating time In an HMC or MD simulation this text box sets the time ps over which the system is heated before the LRM task is launched to obtain averages for the van der Waals Coulombic reaction field and cavity terms The default value for the heating time is 5 ps When the Liaison input file is written the heating time is converted to the value of mxcyc HMC or nstep MD writt
45. button displays a context sensitive menu Other common mouse functions are supported such as using the mouse in combination with the SHIFT or CTRL keys to select a range of items and select or deselect a single item without affecting other items In addition the mouse buttons are used for special functions described later in this chapter These functions assume that you have a three button mouse If you have a two button mouse ensure that it is configured for three button mouse simulation the middle mouse button is simulated by pressing or holding down both buttons simultaneously 2 20 Starting Maestro Before you start Maestro you must first set the SCHRODINGER environment variable to point to the installation directory You can set this variable by entering the following command at a shell prompt csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory You might also need to set the DISPLAY environment variable if it is not set automatically when you log in To determine if you need to set this variable enter the command echo SDISPLAY FirstDiscovery 3 0 User Manual 5 Chapter 2 Introduction to Maestro If the response is a blank line set the variable by entering the following command csh tesh setenv DISPLAY display machine name 0 0 bash ksh export DISPLAY display machine name 0 0 After you set the SCHRODINGER and DISPLAY environment
46. called a Ligand Library file cannot be used by the Pose Viewer but might be appropriate if the output poses are intended for input to a subsequent Glide job or for some other purpose A report file that lists critical information about the scoring of the retained poses is also written Like the output pose file the entries in the report file are ordered by the selected final scoring function e g by GlideScore or by the modified Coulomb van der Waals energy score The file name is jobname rept Keep at most poses This text box limits the total number of the predicted best binding poses written to the output file The default value is 1000 poses This number should be increased in large scale database screens if substantially more than 1000 ligands are docked in individual jobs Keep at most X poses per ligand This text box limits the number of poses per ligand that will be written to the output file The default choice of 1 pose per ligand is intended for use in database screening applica tions A larger value may be appropriate for lead optimization studies or whenever several reasonable poses for an individual ligand are wanted for example to generate a variety of docked poses for study by Liaison or another post docking program 6 7 3 Raw Pose Files Output Pose Files and glide sort In flexible docking runs but not rigid docking runs Glide continually appends good poses to an intermediate jobname raw mae p
47. default number depends on the type of docking specified 88 FirstDiscovery 3 0 User Manual Chapter 6 Glide For flexible docking jobs in general the default is 400 poses If Glide Constraints have been applied to a flexible docking job 40 poses If extra precision XP docking has been selected the number of poses is internally adjusted to a minimum of 800 For rigid docking the default is 100 poses This number is not changed by the appli cation of Glide Constraints The range for this setting is 1 to the value in the Keep ____ initial poses per ligand for refine ment text box 6 6 2 Energy Minimization Section The third stage of the Glide algorithm see Figure 6 2 on page 67 evaluates and mini mizes poses that survive the Refinement Of Initial Poses On Coarse Grid scoring phase The selection options in this section are described below Distance dependent dielectric constant Glide uses a distance dependent dielectric model in which the effective dielectric constant is the supplied constant multiplied by the distance between the interacting pair of atoms This text box allows you to set the dielectric constant to any real value greater than or equal to 1 0 The default setting is 2 0 Do not change this setting because Glide s sampling algorithms are optimized for this value Maximum number of conjugate gradient steps This text box allows you to alter the maximum number of minimization steps used by t
48. default the neighbor list is updated every 10 minimization or dynamics steps Increasing this value updating the neighbor list ess often will speed the calculation but may affect the accu racy of the results Decreasing this value updating the neighbor list more often will slow the calculation but may improve the accuracy Residue based cutoff distance This text box specifies the value for the cutoff distance Increasing the cutoff distance will slow the calculation and require more memory but may yield more accurate results Decreasing the cutoff will speed up the calculation but may reduce the accuracy of the results if significant nonbonded interactions are omitted This is especially true for systems that include formally charged atoms as such systems can have large long range electrostatic interactions 9 4 4 The Fast Multipole Method Panel For large systems the Fast Multipole Method FMM speeds the evaluation of the electro static and van der Waals parts of the molecular mechanics energy by using interacting hierarchical multipoles to approximate the true electrostatic potential When used with periodic boundary conditions the box must be cubic the FMM method requires that the net charge of the system be zero FMM calculations also can be carried out on isolated non periodic systems but this is seldom cost effective except for systems containing tens of thousands of atoms FirstDiscovery 3 0 User Manual 157 Chapter 9
49. energy for the current coordinates Algorithm This option menu selects the minimization algorithm The choices are Truncated Newton TN This is a very efficient method for producing optimized structures and is also the default A short conjugate gradient pre minimization stage is performed first to help improve the convergence of the Truncated Newton algo rithm The Truncated Newton minimization algorithm is not available if the Fast Mul tipole Method FMM has been selected in the Potential folder The Truncated Newton minimization algorithm is not available if the Poisson Boltzmann solver PBF continuum solvation method has been selected Conjugate gradient This is a good general optimization method FirstDiscovery 3 0 User Manual 163 Chapter 9 Energy Minimization Steepest descent This can be a good method for initiating a minimization on a start ing geometry that contains large steric clashes Convergence is very poor towards the end of minimization where the conjugate gradient algorithm should be used Initial step size This text box specifies the initial step size of the minimization cycle The default value is 0 05 but any positive value is allowed Maximum step size This text box specifies the maximum step size of the minimization cycle If the step size exceeds this value the minimization will halt The default value is 1 00 but any positive value is allowed The maximum step size is the
50. entry in the Project Table To perform Molecular Dynamics simulations on a system composed of multiple entries 1 Include only those entries in the Workspace 2 Select Workspace as the Source of job input 10 2 Dynamics Panel Features The Dynamics panel has four tabbed folders Potential Constraints MD Parameters Dynamics FirstDiscovery 3 0 User Manual 165 Chapter 10 Molecular Dynamics Simulations The Potential and Constraints folders are described in Chapter 9 The Constraints folder in the Dynamics panel includes features not available for Energy Minimization Liaison or QSite These are described here along with the MD Parameters folder and the Dynamics folder 10 3 The Constraints Folder In addition to the features described in Section 9 5 on page 160 the following features appear in the Constraints folder for Impact Dynamics and or HMC calculations Constrain all bonds This option is selected by default for Impact Dynamics but is not the default for HMC simulations When selected it constrains all bond lengths to the ideal values defined by the molecular force field For HMC and MD simulations SHAKE is used to constrain the bond length and RATTLE is used to remove the relative motion velocity of the bonded atoms along the interatomic axis Impact Dynamics idynamics lei Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace gt Selected entry In
51. expected to vary for each system studied there are no universal default values Parameter Constraints Fitting jobs will normally derive values for all the parameters appropriate to the selected binding energy model If you want to set and constrain a value for some but not all of the parameters check the box next to it then specify a constraint value for the parameter in the Fitting Parameter text box These boxes do not appear next to parameters not appro priate for the model and also do not appear for Predict jobs for which the Analysis folder lists the derived values under Prediction Parameters Fit or Predict Output This read only text area specifies the name and location of the text file containing the output of the analysis job The file name will be of the form liafit_jobname out or liapredict jobname out where jobname is the name in the Job text box This name must be the same as the name of the Master Liaison Run Directory The output file is written in the Maestro working directory Multiple Fit or Predict tasks having the same jobname will overwrite the previous copy of the output file To prevent this move or rename the files from a terminal window The Fit or Predict output file can be opened from any available terminal window 7 9 2 Ligand Specification Section The bottom section of the Analysis folder identifies the ligands and for Fit tasks their binding energies Specify Ligands By This option menu is e
52. for the structures in the Workspace use the Write Job Files button in the ProteinPrep panel to write the struc ture files 2 Use the protprep command line application or the pprep and or impref com mand line utilities to run specific procedures These commands and their options are summarized below 4 11 1 Usage Summary for protprep The SSCHRODINGER protprep application has command line options corresponding to features of the Maestro ProteinPrep panel The command protprep h displays the usage summary that appears in this section Syntax SSCHRODINGER protprep options input file FirstDiscovery 3 0 User Manual 55 Chapter 4 Protein Preparation input file is the file containing the protein to be prepared or refined This file must be in Maestro format When doing a refinement only job mode refine this file can contain a protein ligand complex Options General Options j jobname 1 ligand file m mode mode mode debug HOST host LOCAL WAIT NICE HELP h Preparation Stage Options min recep only skip sidechain corr cavity 8 12 salt bridge dist ionization range hbond dist 56 Override the default job name derived from input file This allows you to choose an output job name that is different from the input file name Specify a file containing a ligand in the protein s active site This file must be in Maestro format Select mode where mode is one of th
53. have known active ligands and can determine their scores and ranks 4 Extract the selected range of poses from the Maestro output file written by Glide It might be convenient to use the glide sort utility with the n option number of poses to keep glide sort n poses to keep o selected poses file 5 Using the ligand poses prepared according to the steps in the previous section set up a Glide docking job choosing Extra precision as the docking mode 6 Complete Glide setup and run the job 6 3 3 Other Settings Folder Options Displayed structure is This option menu has three choices it is important that the option be selected correctly If the structure currently displayed in the Workspace is only the receptor protein without any ligand set the option menu to Receptor alone 72 FirstDiscovery 3 0 User Manual Chapter 6 Glide If the structure currently displayed is the protein and a ligand choose Receptor plus a single ligand from the option menu The ligand can be but need not be docked or otherwise used in the Glide setup procedure If the currently displayed structure is just a ligand to be docked or scored and this is a Dock one or more ligands job choose Ligand alone from the option menu This option is not available for Set up grids jobs If this is a Dock one or more ligands job and the contents of the Workspace will not be used in the docking you can use any of the options Choose an atom in the ligand mol
54. in file Features of the QSite Constraints folder include two buttons Frozen Atoms Buffered Atoms These buttons open the same panels as the corresponding buttons in the Impact Energy Minimization panel Constraints folder Both panels are described in detail in Section 9 5 on page 160 142 FirstDiscovery 3 0 User Manual Chapter 8 QSite QSite qsite Job gsitetmp Login dya11 Host localhost 1 Source of job input Workspace x Selected entry Incorporate output into project by Appending new entries lt Replacing existing entries Do not incorporate Potential Constraints Minimization Optimization QM Settings Frozen Atoms Buffered Atoms Start Write Job Files Hide Help Figure 8 2 The Constraints folder of the QSite panel 8 5 The Minimization Folder The Minimization folder specifies settings for Impact energy minimization of the MM region of the molecule These settings are not used and no MM minimization is performed if the QM method chosen in the Optimization folder is Single point The Truncated Newton minimization algorithm is not available for QSite In other respects the QSite Minimization folder offers the same functionality as the Impact Energy Minimization panel Minimization folder which is described in detail in Section 9 6 on page 162 FirstDiscovery 3 0 User Manual 143 Chapter 8 QSite QiSite qsite Eei Job gsitetmp Login d
55. known actives e Weight similarity scores using file gridbase wgt e Base penalty value kcal mol Fully penalize ligands with similarity No penalty for ligands with similarity e Reject ligands with similarity Filename of known actives Select a file containing the active compounds to be used in atom pair matching for computing similarity scores For weighted similarity this file should normally be the same one used to calibrate the weights because weights calibrated with one set of actives may not give good results when used with a different set Weight similarity scores using file gridbase wgt Turn this toggle on to specify weighted similarity scoring Note that the weights will be taken from a file produced in a grid generation job run with the Generate Weights toggle on with the same base name as the Glide docking grids and this name is not separately adjustable In other words if you are using docking grids called mybase grd etc and you launch your job from Maestro you must use similarity weights from mybase wgt In order to specify weights from a different file produced in a different grid generation job you must edit your Glide input file by hand and run it from the command line rather than from Maestro Base penalty value The value entered here is P nax in the expression above which is added to the GlideScore of ligands that fall below the specified similarity threshold Smin Th
56. noted below Verlet The widely used velocity Verlet integration algorithm is the default for inte grating the equations of motion in standard Cartesian space molecular dynamics RRESPA The Reversible REference System Propagator Algorithm the other choice offered by Impact for integrating the EOM can be much more efficient By breaking up the integration into large medium and small time steps see the RRESPA update frequencies text boxes this integrator devotes appropriate compu tational power to specific classes of forces and thus to keep the calculation from being dominated by the small time steps needed to accurately integrate the fast motions such as bond stretches In particular RRESPA integrates the fast motions with small time steps and the slow motions far more numerous with larger time steps RRESPA update frequencies If you select RRESPA text boxes for Fast forces Medium forces and Slow forces are enabled When the Fast Multipole Method FMM is also used the forces are separated into three groups those arising from well separated bodies those arising from first and second neighbors that are not very close and those coming from the local expan sions which include bonded terms FirstDiscovery 3 0 User Manual 167 Chapter 10 Molecular Dynamics Simulations Table 10 1 RRESPA Text Boxes Force Interacting Species Default Setting Fast Bonded and short distance electrostatics 4 Medium 1 and 2
57. option if you want nonaromatic five and six membered rings to remain in their input conformation throughout docking Dock each input structure rigidly Rigid docking allows the existing ligand structure to be adjusted but the conformation generation step is skipped Since conformations are not generated the amide and ring conformation options are not available Score each input structure in place scoring output file jobname scor Choose this option if you want to use the input ligand coordinates to position each ligand for scoring This option performs scoring but not docking since other ligand positions are not sampled One use of this capability is to score the cocrystallized ligand in its original or modeled position Another use is to post process ligand poses generated by Glide to obtain additional components of the GlideScore or energy score prediction of the binding affinity The output is written to a file named jobname scor where jobname is taken from the Job text box found at the upper left corner of the panel As in other docking options you can score the displayed ligand and or one or more ligands read from an external file Do not count amide bonds as rotatable This option is available when the score in place option is selected The default is to include amide bonds in the total rotatable bonds count Select this option to exclude amide bonds from the total Scaling of vdW radii for nonpolar ligand atoms As
58. periodic boundary conditions W Use continuum solvation Settings Start Write Job Files Hide Help Figure 9 1 The Potential folder of the Impact Energy Minimization panel Constant dielectric This option calculates the electrostatic interaction between atoms i and j as Ege 332 063762 qq r where E is the electrostatic interaction in kcal mol q and q are the partial atomic charges on atom i and j rj is the distance in between atoms i and j is the Dielectric constant see below A constant dielectric is appropriate for a vacuum gas phase calculation or when an explicit or implicit solvent model is used Distance dependent dielectric This option calculates the electrostatic interaction between atoms i and j as Ea 332 063762 4 q ri where E is the electrostatic interaction in kcal mol qj and q are the partial atomic charges on atom i and j FirstDiscovery 3 0 User Manual 155 Chapter 9 Energy Minimization rjis the distance in A between atoms i and j isthe Dielectric constant see below A distance dependent dielectric is sometimes used as a primitive model for the effect of solvent In this model the electrostatic interaction between a pair of atoms falls off rapidly as the distance between the atoms increases However continuum and explicit solvent models are much better at accounting for solvent effects than a distance dependent dielectric Dielectric constant
59. previously noted Glide does not allow for flexible receptor docking for induced fit docking see Section 6 1 3 but to model a bit of give in the receptor you can scale the van der Waals radii of nonpolar atoms in the ligand and or receptor causing lower penalties for close contacts Scaling of nonpolar receptor atoms must be set up in the Glide Site folder before grid generation is performed Use the Ligand folder options described here to use vdW scaling of nonpolar ligand atoms in docking The Scale radius if Ipartial atomic chargel option defines which atoms are considered suffi ciently nonpolar to be subject to scaling This is the absolute value of the partial charge so the number entered must be positive The default cutoff for ligand atoms in Glide 3 0 is a 84 FirstDiscovery 3 0 User Manual Chapter 6 Glide partial charge with absolute value smaller than or equal to 0 15 electrons The Scale by text box sets the scaling factor The default is 0 80 To turn van der Waals scaling of ligand atom radii off set the scale factor to 1 0 Define a reference ligand When selected this option allows you to specify the conformation position and orienta tion of a reference ligand for Glide to use to assess the accuracy of docking topologically identical ligands Glide reports the rms distance between nonhydrogen atoms of the docked ligand and the reference ligand when the docked ligand and the reference ligand are recognized as being
60. sese 89 scripts command line eeesee 35 A UECII D 22 nli 35 sdconvert LigPrep use of 60 62 Sequence Viewer tede eese 42 sequences identical sss 42 SEI FEIELD 55 intent 28 SGB see Surface Generalized Born SGB SHAKE RATTLE algorithm 160 shortcut keys main window 11 12 Project Table panel 17 side chain cuts eese 150 side chain picking residue selection by 150 SIMU ALI CY ERR 65 similarity scoring eee 98 standard i i metet 98 welghted nieht tie 98 single point energy calculation 145 smoothed grids sese 68 FirstDiscovery 3 0 User Manual Solvation method sss 159 solvation continuum 141 148 156 solvent molecules sss 150 solvent implicit nee 156 standard TS optimization 146 standard precision SP docking mode 69 standard precision Glide docking 72 steepest descent ees 164 stereoizer brief description 61 steric clashes in energy minimization 164 Stop Overall Motion sss 169 SISTI PA 68 structure format conversion 59 Structures building iet 18 20 displaying in sequence
61. specified For other formats only a single file may be specified the Add File button is disabled after the first file is added but the file may contain any number of ligand structures Dock all structures from ligand file Dock range of structures from file When multiple ligands are read from a single Maestro or SD file Glide will Dock all struc tures from ligand file by default Selecting the Dock range of structures from file option instead allows a subset of consecutive structures to be docked numbered as they are listed in the file This facility provides a convenient mechanism for dividing a large input ligand file into subsets for concurrent processing on a multi processor machine provided you have suffi cient licenses to run multiple copies of Glide simultaneously For example you could start a first calculation by clicking the Start button with 1 and 100 entered in the text boxes Then you could enter 101 and 200 change the job name in the Job text box to avoid overwriting output files and click the Start button again to dispatch a second group of ligands Continuing in this way you could quickly submit as many sub jobs as are needed to cover the range of ligands to be docked subject to licensing restrictions Such multiple submissions however are more commonly and more conveniently handled by selecting Write Job Files to write out a single template input file You can then use this template file as input to the pa
62. sulfhydryls of cysteine residues This is accomplished by tightly tethering non hydrogen atoms with a force constant of 10 kcal mol and by minimizing the hydrogens with torsion interactions turned off Each restrained minimization employs a limited number of minimization steps and is not intended to minimize the system completely Subsequent steps restore the torsion potential and use progressively weaker restraints on the non hydrogen atoms hydrogen atoms are always free The force constants employed are 3 1 0 3 and 0 1 kcal mol 52 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation Preparation and refinement the default runs both components This is the recommended mode if you have not yet run any preparation jobs on the protein Separate Preparation only and Refinement only jobs can be run if you encountered a problem in the combined Preparation and refinement job Subsequent Refinement only jobs can be performed after a Preparation and refinement job if water molecules need to be reoriented or if other struc tural adjustments need to be made 4 9 4 Other Options 1 Neutralization zone around the ligand 10 20 A You can also choose a shorter distance 8 12 A or choose Do not neutralize residues 2 Stop minimization when RMSD reaches 0 30 A This is the default value It allows the refinement portion of the job to halt when the average RMSD of the heavy atoms reaches 0 30 A 3 Incorporate results as S
63. the Liaison panel To open the Analysis folder select Analyze results of earlier simulations in the Settings folder This selection enables the Analysis folder and disables the System Parameters and Constraints folders The Analysis folder contains two sections analysis settings and ligand specification 7 9 1 Analysis Settings Section The top section of the Analysis folder selects the type of analysis to be performed and where relevant takes as input values for the LRM coefficients o B and y or the GlideScore model coefficients a and b The Results of the Analysis display area is also located here Analysis type These options select Fit or Predict as the analysis type Fit This option requires a text file containing at least three ligand names and the associated binding energies The specification and format of this file are described below in connection with the Name of Ligand Binding Energy File text box 132 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Liaison Job predict sim Login saunders Host localhost 1 Settings System Parameters Constraints Analysis Analysis type Prediction parameters v Fit Van der Waals alpha 9 Predict Electrostatic beta Binding energy model Cavity gamma 0 LIA equation Sape 0 0 intercept Y GlideScore dabis Specify ligands by Read ligand names from a text file File name of ligand names f E Browse Conma separated ist
64. their element symbol and formal charge 3 Check any metal ions to make sure they are correct If they are the next step in the process is Section 4 7 4 If not you can correct them To correct metal ion atom types 1 In the Build panel click the Atom Properties tab and select Atom Type MacroModel from the Property option menu 2 Find the correct atom type for the metal ion The atom type for metal ions includes both element name and formal charge Atom type numbers are in parentheses 3 Click in the list to select the correct atom type 4 Click on the metal ion to be changed 46 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation 4 7 4 Displaying the Cofactor Cofactors are included as part of the protein but because they are not standard residues it is sometimes necessary to use Maestro s structure editing capabilities to ensure that multiple bonds and formal charges are assigned correctly To display only the cofactor 1 On the toolbar choose Select from the Display only button menu lt q E The Atom Selection dialog box ASD is displayed 2 In the Residue folder choose Residue Type 3 Click the residue type of the cofactor which will be near the end of the list The cofactor is highlighted 4 Click Add then click OK The cofactor is displayed Because the cofactor was chosen by residue type and not mole cule number this method works even if the cofactor is covalently bonded to another
65. variables you can start Maestro using the command SSCHRODINGER maestro options If the SSCHRODINGER directory has been added to your path you only need to enter the command maestro Options for this command are given in the Maestro User Manual The directory from which you started Maestro is Maestro s current working directory and all data files are written to and read from this directory unless otherwise specified see Section 2 8 on page 23 You can change directories by entering the following command in the command input area of the main window cd directory name where directory name is either a full path or a relative path 2 3 The Maestro Main Window The Maestro main window is shown in Figure 2 1 on page 7 The main window compo nents are as follows Title bar displays the project name and the current working directory Auto Help automatically displays context sensitive help Menu bar provides access to panels Workspace displays molecular structures Clipping planes window displays a small top view of the Workspace and shows the clipping planes and viewing volume indicators Toolbar contains buttons for many common tasks and also provides tools for dis playing and manipulating structures and organizing the Workspace Status bar displays the number of atoms entries residues chains and molecules in the Workspace Sequence viewer shows the sequences for proteins displayed in the Workspa
66. variations on the structures eliminate unwanted structures and optimize the structures Many of the steps are optional and are controlled by selecting options in the LigPrep panel or specifying command line options The steps are outlined below Each step is performed by the script or program listed in the step 1 Convert structure format If the input structure file is in SD format it is converted to Maestro format by sdconvert Parities specified in the SD file are converted into chiralities which are stored as properties in the Maestro file 2 Select structures A subset of the input structures can be selected for processing The selection is done by maesubset for Maestro input files and by sdconvert for SD input files 3 Add hydrogen atoms Structures that have implicit hydrogen atoms may need to have hydrogen atoms added before the 3D structures can be minimized Hydrogen atoms are added in a manner that is consistent with a particular force field This step is performed by applyhtreat which is the program used by the Hydrogen Treatment panel in Maestro 4 Remove unwanted molecules If structures have additional molecules included such as counter ions in salts and water molecules these may need to be removed The desalter removes all but the molecule containing the most atoms from each structure 5 Neutralize charged groups 60 FirstDiscovery 3 0 User Manual Chapter 5 Ligand Preparation Charged groups must be
67. 1 Definition of core and rotamer groups 66 FirstDiscovery 3 0 User Manual Chapter 6 Glide Glide Funnel Ligand conformations Stage 1 Site point search Stage 2 Step 2a Diameter test Step 2b Subset test Step 2c Greedy score Step 2d Refinement Stage 3 Grid minimization Stage 4 Final scoring GlideScore Top hits Pose Viewer and report files Figure 6 2 The Glide docking hierarchy scoring function Eldridge et al J Comput Aided Mol Des 1997 11 425 445 Much as for ChemScore itself this algorithm recognizes favorable hydrophobic hydrogen bonding and metal ligation interactions and penalizes steric clashes This stage is called greedy scoring because the actual score for each atom depends not only on its position relative to the receptor but also on the best possible score it could get by moving 1 A in X Y and or Z This is done to mute the sting of the large 2 jumps in the site point ligand center positions The final step in Stage 2 is to re score the top greedy scoring poses via a refinement procedure Step 2d in which the ligand as a whole is allowed to move rigidly by 1 A in the Cartesian directions Only a small number of the best refined poses typically 100 400 are passed on to the third stage in the hierarchy energy minimization on the pre computed OPLS AA van der Waals and electrostatic grids for the receptor The energy minimization typic
68. Discovery 3 0 User Manual Chapter 3 FirstDiscovery from the Command Line 3 4 3 Liaison Liaison uses its own scripts for running calculations from the command line You can use Maestro to write the scripts or you can modify the template scripts found in the directory SSCHRODINGER impact vversion_number samples liaison See the Maestro online help or the FirstDiscovery Command Reference Manual for more information The simulate_jobname script ensures that the free and bound input files are run for each ligand receptor pair and are named appropriately To run a Liaison calculation using job files you have written from the Maestro interface enter the following in a terminal window simulate jobname Once the Liaison simulations are complete you can use the analyze jobname script to do either of the following Mine data and fit or predict mined results to known binding energies for the specific ligand receptor pairs Predict the binding energies of the test ligands given known values of alpha beta and gamma typically those calculated by a previous fit However it is more convenient to run the very fast fit and predict calculations directly from the Maestro interface Distributed processing of Liaison simulation jobs is available from the GUI only See Section 7 5 3 44 QSite QSite jobs have two input files one for Impact which runs the molecular mechanics part of the calculation and one for Jaguar wh
69. Figure 2 3 The Build panel You can also draw a structure freehand by choosing an element from the Draw button menu on the Build panel toolbar and then drawing the structure In the Atom Properties folder you can change the properties of the atoms in the Work space For each item on the Property menu Element MacroModel Type Partial Charge PDB Atom Name Grow Name and Atom Name there is a set of tools you can use to change the atom properties For example the Element tools consist of a periodic table from which you can choose an element and pick an atom to change it to an atom of the selected element Similarly the Residue Properties folder provides tools for changing the properties of resi dues the residue number the residue name and the chain name To adjust bond lengths bond angles dihedral angles and chiralities during or after building a structure use the Adjust panel which you open from the Edit menu on the main menu bar or with the Display Adjust panel button on the Build panel toolbar 4 FirstDiscovery 3 0 User Manual 19 Chapter 2 Introduction to Maestro The toolbar of the Build panel provides quick access to tools for drawing and modifying structures and labeling atoms See Section 2 3 2 on page 8 for a description of the types of toolbar buttons The toolbar buttons and their use are described below HEA dr H 20 Draw Draw structures freehand in the Workspace Menu button with a list of elements t
70. FirstDiscovery 3 0 User Manual Copyright 2004 Schr dinger LLC All rights reserved Schr dinger FirstDiscovery Glide Impact Jaguar Liaison LigPrep Maestro Prime QSite and QikProp are trademarks of Schr dinger LLC MacroModel is a registered trademark of Schr dinger LLC To the maximum extent permitted by applicable law this publication is provided as is without warranty of any kind This publication may contain trademarks of other companies Revision A June 2004 Contents Chapter T IntrOQUCtlOli 1 eoe ete eroe eee eto a eran neve ev oe aceto ee too vna eire reser ue 1 1 1 Document Conventions 5 3 1 tot tetrt eher ce EE PERSE PRESE ENTER eA E EES 2 1 2 Introduction to FustDiscovery Panels ttr ettet 2 12 1 Job OpUODS rester ee ext PE rh er ER E E EREE 2 1 2 2 Panel Controls and Tabbed Fold rs eres 4 1 2 5 Start Write Hide and Help error acai aei 4 Chapter 2 Introduction to Maestro eec eee cete ee esee ee eene enne enne tne stes nest 5 2 1 General Interface BeliaviOt iet ette tete bee nr Pott e calo ise EEE 5 2 2 Starting Ma365tro s nieder mre tesi e Ere C ES ERE ERE Sia 5 2 3 The Maestro Main Window nne het tede eie tte renes 6 2 5 1 The Menu Dabo orem pr roe cett o oce rei aeri tere mee tetti tn 7 2 3 2 Phe TOBIDAE oim tte oet hace ee eel a ened ets 8 2 3 3 Mouse Functions in the WorkSpace 2 n eerte 11 2 34 Shortcut Key Comb
71. Glide function Using Glide for docking ligands to a receptor is a two step process Receptor grids must be generated before ligands can be docked Glide performs both these functions The first option in the Settings folder Choose Glide function specifies whether Glide is to Set up grids or Dock one or more ligands A protein or protein ligand complex must be included in the Workspace before you set up grid generation As the name implies this job only calculates the scoring grids for receptor and saves them to disk Once this job is completed subsequent Dock one or more ligands jobs can perform ligand docking using this set of receptor grids 70 FirstDiscovery 3 0 User Manual Chapter 6 Glide 6 3 2 Docking Mode Options and Using Extra Precision Mode Choose docking mode This menu sets the mode for the Glide docking job Either Standard speed and precision SP or Extra precision XP is available The latter provides better sampling but requires greater CPU time Generally you should run your database through the Standard mode first then take the top 10 to 30 of your final poses and run them through Extra preci sion so that you perform the more CPU time intensive docking simulation on worthwhile poses The Extra precision option is active only when the Choose Glide function selection is Dock one or more ligands Glide glide Host localhost 1 settings site ugana Searing output Constraints simitarity C
72. Hydrogen Treatment from the Edit menu Hydrogen atoms can also be added or removed using the command line tool applyhtreat which is described in the Maestro User Manual and the LigPrep User Manual 5 2 LigPrep The Schr dinger ligand preparation product LigPrep is designed to prepare high quality all atom 3D structures for large numbers of drug like molecules starting with 2D or 3D structures in SD or Maestro format LigPrep can be run from Maestro or from the command line FirstDiscovery 3 0 User Manual 59 Chapter 5 Ligand Preparation LigPrep is licensed separately from other Schr dinger products The MacroModel commands premin and bmin require LigPrep licenses when run in a LigPrep context and are limited to a restricted set of commands when run using a LigPrep license For more information about obtaining LigPrep contact help schrodinger com The simplest use of LigPrep produces a single low energy 3D structure with correct chiralities for each successfully processed input structure LigPrep can also produce a number of structures from each input structure with various ionization states tautomers stereochemistries and ring conformations and eliminate molecules using various criteria including molecular weight or specified numbers and types of functional groups present 5 2 4 The LigPrep Process The LigPrep process consists of a series of steps that perform conversions apply correc tions to the structures generate
73. K increments of 0 50 K 50 100 K 250 300 K Given that the Liaison panel has default heating time of 5 00 ps time step of 0 002 ps and number of MD steps per MC step of 5 then mxcyc 5 000 ps 0 002 ps 5 500 500 divided by 6 increments is 83 rounded steps per increment Simulation time In an HMC or MD simulation this text box sets the simulation time for the LRM task used to determine the averages for the van der Waals Coulombic reaction field and cavity terms The default value for the simulation time is 5 ps When energy minimization is used for sampling no heating is done but a short pro forma HMC simulation mxcyc 10 is carried out at 10 K to obtain the needed averages for the Liaison interaction quantities When the Liaison input file is written the simulation time is converted to the value of mxcyc HMC or nstep MD that is written to the LRM task The table below shows how the conversion is made 128 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Task Conversion Formula HMC Simulation Time 2 mxcyc nmdmc delt MD Simulation Time 2nstep delt Min N A mxcyc of HMC cycles nmdmc of MD steps per MC cycle nstep ff of MD steps delt time step in ps delt is 0 002 ps for HMC and 0 001 ps for MD The default 0 002 ps time step for HMC and 0 001 ps time step used for Liaison dynamics MD jobs are not modifiable inside Maestro but can be edited by hand in
74. Molecules seen 41 4 5 5 Delete Remaining Unwanted Waters essere 42 4 6 Simplifying the Protein Complex 0 cccccceeseeseesseeseceeeeseeeeeeseeeeeeseeeeeeseeneeeaeens 42 4 6 1 Determining Whether the Complex Is a Multimer 42 4 6 2 Retaining Needed S b nits eere reete es 43 4 7 Adjusting the Protein Metal Ions and Cofactors esee 45 4 7 1 Proteins That Already Include Hydrogen Atoms 45 4 7 2 Checking the Protein Structure for Metal Ions and Cofactors 45 47 5 Adjusting Metal Tonsen ie enie n reenen E en pR EEEE RENTE 45 4 7 4 Displaying the COfPaetoE eere eme raten rer errare rine 47 4 7 5 Adjusting Cofactor Atom and Bond Properties sess 47 Z8 Adjus ne the 198Bd n i erre retener eere ro EE REK PEE e Peer tene aed 49 4 8 1 Adjusting Ligand Atom and Bond Properties sesssss 49 4 8 2 Manually Deleting Explicit Ligand Metal Bonds 50 4 8 3 Checking for Other Protein Ligand Bonds sss 51 FirstDiscovery 3 0 User Manual Contents 4 9 Running ProteinPrep on the Structures sci isise sinnsir ienis ieia ina 51 49 1 Entering Job Seve reme eret iot eee ee erp Parere eg 52 4 02 Defining the DIgatid eee tetris E ER EEE 52 4 9 5 Choosing a Proce CUMS ennienni o p Fer REA
75. NO PER Ea 52 4 9 4 Oher ODUGOHBS iecore tn Ete Dv eve En na nare ri gea bue aere sie dod 53 49 5 Launching the ProtembPrep Job rere emen 53 4 9 6 Output Job Tales e Ee Myr keen ce etc EREE aad PEU HER E REEL ESSE 53 4 10 Checking the Output SEGETES cote ere irte a re rete 54 4 10 1 Checking the Orientation of Water Molecules sss 54 4 10 2 Resolving H Bonding Conflicts essere 55 4 11 Command Line Protein Preparation eie tert tentia 55 4 11 1 Usage Summary Tor protpEep easier rure nere tingere nd 55 4 11 2 Usage Summary Tor pD GD oec er etre re reme een 57 4 11 3 Usage Summary Tor 3mpEef tete ripetere petro pito Regis 58 Chapter 5 Ligand Preparation eee eee e ee eee eee e eene teste setas ta se tna etna 59 5 1 Ligand Preparation Clhecklist eee nee eet eem 59 oy 2 E PTE 59 5 2 The Lag Prep Prot sS iced tet eet enge 60 5 2 2 The LigPrep Pariel eee tho noter erede 62 5 3 The Ionization State Expander 1onizer eere 63 Brad HC mc 65 6 1 lontod ctiom to Glide i nen eerte rec Ee as Mea eee 65 6 1 T lide C Ons TEA IME Sc o oor EE ev tte easet ie e Gere Rees 68 6 1 2 Glide Extra Precision Mode sess 69 6 1 3 Glide Prime Induced Pit 2 5323 00 2 2 rr rtr riter re etes 69 6 2 The Glide P tiel tiere er der t terere e
76. PK a On the toolbar choose Molecules from the Draw atoms in CPK button menu 2 b Click on an atom in the ligand that was not deleted to display it in CPK c If there is a cofactor click on an atom in that molecule as well d Click the toolbar button a second time to leave the Draw atoms in CPK pick state FirstDiscovery 3 0 User Manual 43 Chapter 4 Protein Preparation 3 Redisplay the protein backbone On the toolbar choose Protein Backbone from the Also display button menu EIE al Making just the backbone visible will provide enough information without unduly cluttering the Workspace 4 Assign coloring by Chain Name On the toolbar choose Chain Name from the Color all atoms by scheme button menu amp 5 Delete duplicate protein chains a On the toolbar choose Chains from the Delete button menu b Click on a backbone atom in each protein chain you want to delete 6 Delete duplicate ligands and cofactors a On the toolbar choose Molecules from the Delete button menu b Click on an atom in each ligand or cofactor to be deleted Note If you make a mistake you can undo your last action by clicking the Undo button on the toolbar Em 7 When finished redisplay the rest of the protein On the toolbar choose All from the Display only button menu 4 E 8 Put all atoms including the ligand and any cofactors back into wire frame On the toolbar double click the Draw bonds in wire button
77. Pick to apply the current hydrogen treatment Menu button with a pick menu and an item to open the Atom Selection dialog box Same as the Add hydrogens button on the main toolbar FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro 2 6 Selecting Atoms Maestro has a powerful set of tools for selecting atoms in a structure that takes advantage of chemical information about the structure These tools are embedded in each panel in which you might need to select atoms to apply some operation Once you have chosen an operation you can use the tools to select or pick the atoms to which to apply the opera tion To select all atoms in a molecule a chain a residue or an entry you can choose a pick state using the Pick menu Once you have chosen the pick state you can click on an atom in the Workspace and all the atoms that belong to the same structural unit as defined by the pick state are selected For example if you choose Residue and click on any atom in a glycine residue all the atoms in that glycine residue are selected To select individual atoms choose Atoms from the Pick menu The Pick menu varies from panel to panel because not all pick states are appropriate for a given operation For example some panels have only Atoms and Bonds in the Pick menu To make atom selections based on more complex criteria such as all carbon atoms in a protein backbone you can use the Atom Selection dialog box To open this dialog bo
78. SD In the Proximity dialog box a Select Beyond enter a distance in the text box and select Angstroms b Under Fill select Residues and Exclude source This keeps the ligand itself from being deleted c Click OK to exit the Proximity dialog box 4 In the Select to Delete ASD click the Residue tab choose Residue Type and select HOH Click Intersect The ASL box will contain an expression similar to not mol num 2 and fillres beyond 5 mol num 2 AND res ptype HOH and most of the water oxygens are marked in the Workspace 5 Click OK to delete the selected water molecules 4 5 5 Delete Remaining Unwanted Waters After deleting water molecules beyond distance dist A from the ligand examine the Work space and delete any remaining water molecules you do not want to keep 1 On the toolbar choose Molecules from the Delete button menu X 1 2 Click on an oxygen to delete that water molecule When you have removed all but the desired waters continue with Section 4 6 4 6 Simplifying the Protein Complex 4 6 Determining Whether the Complex Is a Multimer To determine whether the ligand receptor complex is a multimer compare the chains that appear in the sequence viewer If there are two or more chains with identical sequences the complex may be a multimer If this is the case there may be duplicate copies of the binding site of interest with duplicate chains forming the duplicate binding sites
79. Trun cated Newton algorithm and specifies the distance beyond which forces will be treated as long range that is updated every n steps as specified in the previous option and estimated between updates 164 FirstDiscovery 3 0 User Manual Chapter 10 Molecular Dynamics Simulations 10 1 Using the Dynamics Panel Use the Impact Dynamics panel to set up and run an Impact Molecular Dynamics MD simulation on the Workspace structure Molecular Dynamics simulations examine stable ground state molecules by applying Newton s equations of motion The constant volume and temperature NVT ensemble is the default ensemble for MD simulations The constant volume and energy NVE and constant pressure and temperature NPT ensem bles are also supported NPT simulations require the use of periodic boundary conditions see Section 9 4 5 on page 158 Such calculations often but not always use explicit solvent see Chapter 12 To open the Impact Dynamics panel In the Maestro Applications menu choose Dynamics from the Impact submenu In the upper part of the panel are the standard FirstDiscovery panel options for Job name Login and Host as well as Source of job input and Incorporate output into project by For a description of these options see Section 1 2 The default job name for Impact Molecular Dynamics jobs is impacttmp The input for an Impact Molecular Dynamics job can be either the contents of the Work space or a single
80. User Manual or the Maestro online help for more information 106 FirstDiscovery 3 0 User Manual Chapter 6 Glide PoseWrite posewrite Append Figure 6 15 The PoseWrite panel 6 10 2 The PoseWrite Panel The PoseWrite panel allows you to write out to a Maestro file the pose file structures selected for display in the Glide Pose Viewer panel To open the PoseWrite panel click Write Displayed Poses on the Glide Pose Viewer panel To save a file in the current directory enter the name in the File text box and press the ENTER key or click the Write button The file will be written using the current settings see Append below Maestro accepts absolute e g home joe filel mae or rela tive e g file1 mae file names If you are unsure which directory to use or if you are concerned about overwriting an existing file click the Write To button The Write Pose File file selector panel is displayed When you locate the directory and determine that your file name is unique type the name in the Selection text box and press ENTER or click OK For more information on using a file selector click the Help button on the Write Pose File panel Append When the Append button is enabled the poses currently selected on the Glide Pose Viewer panel are appended to the file whose name appears in the File text box When the button is deselected the file overwrites any existing file of the same name 6 11 Glide Utilities
81. X would prevent the docking of the DuPont Merck cyclic urea that displaces this water In other cases removing waters might enable you to find ligands capable of replacing the missing waters An alternative approach for IHPX would be to prepare versions of the protein with and without the flap water and to dock ligands against both In our database screens for 1HPX excellent rank orders were found for the known ligands even though the flap water was removed 4 5 3 Deleting All Water Molecules If you decide to delete all waters choose Waters from the Delete button menu on the toolbar All water molecules are deleted Skip to Section 4 6 4 5 4 Deleting Distant Water Molecules If you think you may want to keep one or more waters begin by removing those that are farther than dist A from the ligand This task can be performed using the Commands text box in the lowest part of the Maestro main window to enter a command such as delete res HOH and beyond dist mol n molnumlig where molnumlig is the molecule number of the ligand Alternatively use the Delete button and the Atom Selection dialog box ASD 1 Choose Select from the Delete button menu on the toolbar The Select to Delete ASD is opened FirstDiscovery 3 0 User Manual 41 Chapter 4 Protein Preparation 2 In the Molecule folder choose Molecule Number and enter the ligand s molecule number Click Add 3 Click the Proximity button in the lower section of the A
82. a grid The grid spacing controls both the accuracy of and time required for the PBF calculation The FirstDiscovery 3 0 User Manual 159 Chapter 9 Energy Minimization default is to use a Low resolution grid which should suffice for most protein work If needed greater accuracy can be achieved by setting this option menu to Medium or High PBF Displacement Threshold Use this text box to specify how far A any atom may move from the coordinates used in the previous PBF calculation before a new PBF calculation must be performed If no atom has moved this distance the previously calculated PBF energy and forces are used 9 5 The Constraints Folder The Constraints folder is used to set up Impact atom constraints and bond constraints Bond constraints Molecular dynamics and hybrid Monte Carlo simulations can use the SHAKE RATTLE algorithm to constrain bond lengths When setting up these jobs from the GUI you can choose to constrain all bonds the default for MD or not to constrain any bonds the default for HMC These options are discussed in Section 10 3 on page 166 Atom constraints Impact Energy Minimization Molecular Dynamics and Hybrid MC jobs as well as Liaison simulations and QSite calculations can include atom constraints Specified atoms can be frozen at their input coordinates frozen atom constraints or harmonic force constraints buffered atom constraints can be applied to keep them near their input positions
83. accuracy of the PBF calculation and the time required The default Low resolution suffices for most protein work If needed greater accuracy can be achieved by choosing Medium or High resolution Displacement threshold This text box specifies how far in A any atom may move from the coordinates used in the previous PBF calculation before a new PBF calcula tion must be performed If no atom has moved this distance the previously calcu lated PBF energy and forces are used In other respects the QSite Potential folder offers the same functionality as the Impact Energy Minimization panel Potential folder which is described in detail in Section 9 4 on page 154 8 4 The Constraints Folder The QSite panel Constraints folder is used to apply constraints to the Cartesian coordi nates of selected atoms in the MM and or the QM region Specified atoms can be frozen at their input coordinates frozen atom constraints or they can be constrained to remain near their initial coordinates by applying a harmonic force buffered atom constraints In QSite frozen atom constraints can be applied to atoms in both the QM and the MM regions Buffered atom constraints are used only when they are applied to MM region atoms if applied to QM region atoms they are ignored Atom constraints in QSite for atoms in the QM as well as the MM region must be set using the Constraints folder They cannot be set using an amp coord section in the jobname jaguar
84. aces shes tee E e estne oie eae 116 7 2 4 Liaison Simulation Requirements etcetera 117 1 9 MAGS OH Zn aby SIS eee cie end ret dro od RU E EREID 118 7 3 1 Fitting the Simulation Results to Experimental Data 118 7 3 2 Predicting Binding Affinities of New Ligands sss 119 7 4 The Liaison Panel aset ier te eae euet eh olascteoases a ir aeea iE iE Eai vee 119 7 9 The Setungs Boldet sss ie eere tente repertas et bare cube denote e MES 120 7 6 The System Folder beh etie retener rH e Hist yt 122 7 6 1 Multiple Ligands Single Receptor nete 123 7 6 2 Single Ligand Single Receptor seen 124 vi FirstDiscovery 3 0 User Manual Contents 7T The Parameters Folder 25 eaaet petere Paste ee aeta ity 125 TIT I Sampling Metholl 1o beret rere be ri o eee itan 125 7 7 2 Ligand Simulation and Ligand Receptor Simulation 127 7 0 Ipe Constants Pold t e eo eee rrt eter tette amen e exer repe ago 130 17 9 TG Analysis Polder ecc ree one roe n ES RR REPE DEPRIS USES ERE O E E 132 TIA Analysis Settings SecHOD coser ene teer reti ete enero UR 132 79 2 Lagand S peciicavion SeGtion eedem tette 134 7 10 Running Liaison as a Stand Alone Program eee 136 7 11 Kiling Liaison Jobs eene ciere nt te Ron rrt preis 137 Chapter 8 QSite T 139 Bil Using OSes cscs cedes eich
85. alling FirstDiscovery and other Schr dinger software see the Schr dinger Product Installation Guide The ionizer must be run from the command line as follows S SCHRODINGER utilities ionizer options The options are listed in Table 5 1 Table 5 1 Summary of ionizer Options Option Description h help Show this usage summary message doc Show more detailed usage message v ver version Show program version information j job jobname jobname Base name of job No default must be specified unless all essential files are specified i in infile infile Default is jobname mae o out outfile outfile Default is jobname ion mae b bad badfile badfile Default is jobname ion bad mae FirstDiscovery 3 0 User Manual 63 Chapter 5 Ligand Preparation Table 5 1 Summary of ionizer Options Continued Option Description 1 log logfile logfile Default is jobname 10g use 1 to log to screen ph value Effective pH of active site default 7 0 pht phthresh maxdiff pH difference threshold default 2 0 For pH based ion state rejections where maxdiff is the difference limit on de protonated IpKa pHl pkt pkthresh maxdiff Strong weak pK threshold no default Overrides pH based rejection mode reject on pKa values only no pH where maxdiff is the limit on de protonated pKa differ ences mi maxions count Maximum number of ionizations default 4 mq maxabstotq charge Maximum absolute tota
86. ally begins on FirstDiscovery 3 0 User Manual 67 Chapter 6 Glide a set of van der Waals and electrostatic grids that have been smoothed to reduce the large energy and gradient terms that result from too close interatomic contacts It finishes on the full scale OPLS AA nonbonded energy surface annealing This energy minimi zation consists only of rigid body translations and rotations when external conformations are docked When conformations are generated internally however the optimization also includes torsional motion about the core and end group rotatable bonds Unless you specify otherwise a small number of the top ranked poses are then subjected to a Monte Carlo procedure in which alternative local minima core and rotamer group torsion angles are examined to try to improve the energy score Finally the minimized poses are re scored using Schr dinger s proprietary GlideScore scoring function GlideScore is based on ChemScore but includes a steric clash term and adds buried polar terms devised by Schr dinger to penalize electrostatic mismatches The choice of best docked structure is made using a model energy score Emodel that combines the energy grid score the binding affinity predicted by GlideScore and for flexible docking the internal strain energy for the model potential used to direct the conformational search algorithm Glide also computes a specially constructed Coulomb van der Waals interaction energy score t
87. and exporting structures These actions can also be performed from the Project Table panel For more information see Section 2 4 on page 12 Edit menu allows you to undo actions build and modify structures define com mand scripts and macros and find atoms in the Workspace Display menu provides access to panels that control the display of the contents of the Workspace to commands for the display of panels and to options for the display of main window components Your choice of main window components displayed is persistent between Maestro sessions Tools menu provides access to panels for grouping atoms for measuring for aligning and superpositioning structures and for viewing and visualizing data Applications menu provides access to panels for setting up submitting and mon itoring jobs for all Schr dinger s computational programs Some products have a submenu from which you can choose the task to be performed Help menu provides access to the Help panel and to a control for the display of Balloon help tooltips 2 3 2 The Toolbar The main toolbar contains buttons for performing common tasks There are three kinds of buttons on the toolbar Those that perform simple tasks like clearing the Workspace Those that show and hide panels or open dialog boxes Those that display a menu when you click and hold The third type of button is called a menu button and has a triangle in the lower right corner
88. ank files extensions pdb or ent Ligand file name This text box allows you to specify the location of the ligand if it is not already loaded into the Workspace There are two buttons to the right of the text box Read and Browse If there is no displayed ligand the selected ligand is added to the Workspace Click Browse to browse for the ligand file or enter the file name in the text box and click Read Structure number in ligand file If the ligand file contains multiple structures you can specify the structure to be used as the ligand by entering the number that corresponds to its position in the file The default is to use structure 1 6 4 5 The Active Site Residues Panel Use the Active Site Residues panel to define selected active site residues of a receptor for a Glide calculation The centroid of the selected residues is then used to center the Glide grid boxes To open the panel select Active site residues in the Site folder and click Specify Active Site Residues The selection options of the Active Site Residues panel are described below Active site residues list The text area in the upper portion of the panel lists the active site residues that are currently defined The list keeps track of the selections made and displays them Items displayed in this list can be selected for deletion see below Active Site Residues activesiteres E Define active site residues W Pick Residues Select Delete Delet
89. ar mechanics force field used by Impact The OPLS AA all atom force field is the only choice for FirstDiscovery and Impact calculations For Liaison and Basic Impact calculations set up from Maestro only the OPLS AA 2001 force field is supported For QSite calculations set up from Maestro only the OPLS AA 1999 force field is supported See the FirstDiscovery Command Reference Manual for information about options from the command line Parameter file This text box allows you to specify a file containing the molecular mechanics parameters to be used by Impact However you will usually not need to change the default value The default molecular mechanics parameters are stored in a file called paramstd dat that is provided in the FirstDiscovery distribution Electrostatic treatment This option menu offers two methods for calculating the electrostatic component of the molecular mechanics energy 154 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization Impact Energy Minimization imini Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace gt Selected entry Incorporate output into project by Appending new entries Replacing existing entries Do not incorporate Potential Constraints Minimization Force field OPLS AA Electrostatic treatment Constant dielectric Dielectric constant 1 0 LJ Use non bonded cutoffs Use fast multipole method L Use
90. ariety of molecular fragments from which to build a struc ture To place a fragment in the Workspace 1 Select Place 2 Choose a fragment library from the Fragments menu 3 Click a fragment 4 Click in the Workspace where you want the fragment to be placed There are several options for adding to a fragment that you have placed Place another fragment and connect them using the Connect amp Fuse panel which you open from the Edit menu on the main menu bar or with the Display Connect Fuse panel on the Build toolbar yK Replace one or more atoms in the existing fragment with another fragment by select ing a fragment and clicking in the Workspace on the main atom to be replaced Grow another fragment by selecting Grow and clicking the fragment you want to add in the Fragments folder Grow mode uses predefined rules to connect a fragment to the grow bond The grow bond is marked by a green arrow The new fragment replaces the atom at the head of the arrow on the grow bond and all atoms attached to it You can change the grow bond by clicking on the desired grow bond in the Workspace The arrow points to the atom nearest to where you clicked 18 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Build build sj El x Z IX edequ 5 adah Atom Residue Properties Properties H N H Kew ad OH whole Der H Grow Direction forward Joining Geometry anti
91. asis set from the Basis set menu Delete To remove a specific ion from the QM region select the ion in the ions list and click Delete Delete All Click Delete All to remove all ions from the QM region 152 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization 9 1 Basic Impact Applications Basic Impact Applications are general purpose molecular mechanics simulations that you can launch from Maestro or from the command line as described in Chapter 3 There are four Basic Impact applications Energy Minimization Molecular Dynamics Hybrid Monte Carlo Soak which will be described in the following chapters For an extensive set of examples of input files for Basic Impact applications see Appendix C of the FirstDiscovery Command Reference Manual The Command Reference Manual is provided on disk with the FirstDiscovery distribution and is also available at Schr dinger s support webpage http www schrodinger com Support pdf html 9 2 Using the Energy Minimization Panel The Impact Energy Minimization panel is used to set up and run an Impact energy minimi zation calculation on the structure in the Workspace To open the Impact Energy Minimization panel In the Maestro Applications menu choose Minimization from the Impact submenu In the upper part of the panel are the standard FirstDiscovery panel options for Job name Login and Host as well as Source of job input and Incorporate output into pro
92. ate binding sites 43 duplicate chains 42 duplicate poses eoe teres 90 Dynamics folder suse 170 dynamics simulations cece 165 E electrostatic grids ees 68 electrostatic treatment essee 154 constant dielectric ss 155 distance dependant dielectric 155 Enmodel 4 ueeautee a re cni 68 87 enclosing box sesess 75 76 96 end of ligand file ess 83 energy C TTEN P 89 antertial 4 eei ehe 87 internal strain eee 68 nonbonded interactions 87 energy change criterion 164 energy grid SCOTE usc enechiteitis 68 energy minimization Hore pue 162 steric clashes Ih ete iter 164 enrichment factor eese 68 entries Project Table 12 including excluding and fixing 16 IDGrpilg eene ninetes 139 selecting sees 15 16 uu M M 14 environment variables DISPLAY aen ipuinera Ennn r E E 5 6 SCHRODINGER sj sciscisscestdedississesectencss 5 6 ur M 13 14 Equations of Motion EOM 167 Ewald long range correction 159 Ewald summation sess 140 excluded entries explicit solvent urns tr eterne extra precision XP mod
93. bed in the Impact Dynamics Panel and Impact Dynamics Folder help topics be used for this and any other explicit solvent systems FirstDiscovery 3 0 User Manual 177 Chapter 12 Soak Add Explicit Water Solvent Soak isoak E E xi Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace gt Selected entry Incorporate output into project by Appending new entries Replacing existing entries lt gt Do not incorporate Soak Solvent type SPC water Solvent density 1 00 Box X dimension 18 62 Box Y dimension 18 62 Box Z dimension 18 62 Start Write Job Files Hide Help Figure 12 1 The Soak panel 12 2 Soak Panel Features The Soak panel has one tabbed folder with the following selection options Solvent type At present the only solvent type that can be added using Soak is SPC Simple Point Charge water Solvent density This text box specifies the density of solvent to be placed around the solute units g cm The default is 1 00 Box X dimension Box Y dimension Box Z dimension Use these three text boxes to specify the required size of the solvent box in The minimum size for any dimension that Maestro will use is 18 62 These values also update the size of the simulation box when periodic boundary conditions are applied See the discussion of periodic boundary conditions in Section 9 4 5 on page 158 178 FirstDiscove
94. below Displayed structure includes the ligand Select this option if the ligand to be simulated is included with the receptor structure in the Workspace Maestro then activates the Select Ligand By Picking an Atom button and expects you to pick an atom to identify the ligand This will be the only ligand simulated Select ligand molecule by picking an atom This button is active when Displayed structure includes the ligand is selected To select the ligand click on an atom of the Workspace structure This visually marks the selected structure using a blue Ball amp Stick representation and everything else is taken to be the receptor The ligand must be marked in this manner or Maestro will consider it as part of the receptor and will be unable to minimize or simulate any ligand in the space already occupied by this ligand Format of ligand file The file format needs to be defined when the ligand is not being taken from the Work space i e when Displayed structure includes the ligand is not selected Liaison supports the three file formats listed below for reading structures from local or network mounted disks Liaison does not support Mol2 formatted files and will not accept structures with explicit lone pairs Remove them via the Hydrogen Treatment menu before submitting the Liaison job Maestro Maestro written files extensions mae out or dat MDL SD SD formatted files extensions mo1 for single structure files and s
95. ce Command input area provides a place to enter Maestro commands You can control the display of any of the last five components from the Display menu 6 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Title bar Auto Help text area Menu bar Workspace aestro zone1 t yall Tutorials GuickTopics Maestro version 6 5 00 Maestro Project Edit Display Tools Applications Toolbar Atoms 1716 1716 Entries 1 1 Res 106 Chn 3 Mol 3 AllAtom1 D gt Al 1Atom1 SIQAEEWYFGKITRRESERLLLNAENPRGTFLYRESEAYCLSVSDFDNA AllAtom1 AllAtoni VEEI i aun 7 Viewing volume indicator Sequence viewer Status bar Command inputarea Clipping plane Figure 2 1 The Maestro main window When a distinction between components in the main window and those in other panels is needed the term main is applied to the main window components e g main toolbar 2 3 1 The Menu Bar The menus on the main menu bar provide access to panels allow you to execute some commands and control the appearance of the Workspace The main menus are as follows Maestro menu allows you to save or print images in the Workspace execute sys tem commands save or load a panel layout set preferences set up Maestro com mand aliases and quit Maestro FirstDiscovery 3 0 User Manual 7 Chapter 2 Introduction to Maestro Project menu provides access to many project related actions such as opening and closing a project and importing
96. conformers this requires that they be topologically equivalent and that the ordering of corresponding atoms be the same When this option is on the Specify Ligand button will be active enabling you to open the Reference Ligand panel 6 5 2 The Reference Ligand Panel The Reference Ligand panel defines the reference ligand Glide uses to compute rms comparisons to conformationally related docked ligands Note that if you want a calcu lated rms for the reference ligand itself make sure it is first in the ligand list To open the Reference Ligand panel select Define a reference ligand in the Ligand folder and click Specify Ligand The selection options of the Reference Ligand panel are described below Use displayed ligand This button requires that the Workspace structure contain a ligand and that the ligand already be identified e g via the Choose an atom in the ligand molecule button in the Glide Settings folder The displayed ligand is then used as the reference ligand Reference Ligand refligand ENE Specify reference ligand ww Use displayed ligand Q Use entry name Use ligand from external file Format Maestro Ligand file name rial tutorial structures H01 H20 lig mae Structure number in ligand file 1 Hide Help Figure 6 8 The Reference Ligand panel FirstDiscovery 3 0 User Manual 85 Chapter 6 Glide Use entry name To select an entry in the Project Table as the reference ligand s
97. core by a rotat able bond but does not contain additional rotatable bonds The core is what remains when each terminus of the ligand is severed at the last rotatable bond Carbon and nitrogen end groups terminated with hydrogen CH NH NH are not considered rotat able because their conformational variation is of little significance In Figure 6 1 the four central torsions are part of the core and the methyl groups are not considered rotatable During conformation generation each core region is represented by a set of core confor mations the number of which depends on the number of rotatable bonds conformation ally labile 5 and 6 membered rings and asymmetric pyramidal trigonal nitrogen centers in the core This set typically contains fewer than 500 core conformations even for quite FirstDiscovery 3 0 User Manual 65 Chapter 6 Glide large and flexible ligands and far fewer for more rigid ligands Every rotamer state for each rotamer group attached to the core is enumerated The core plus all possible rotamer group conformations is docked as a single object in Glide Glide can also dock sets of pre computed conformations However Glide offers its greatest value when flexible docking is used to generate conformations internally For each core conformation or for rigid docking each ligand an exhaustive search of possible locations and orientations is performed over the active site of the protein The sea
98. corporate output into project by Appending new entries Replacing existing entries Do not incorporate Potential Constraints MD Parameters Dynamics W Constrain all bonds SHAKE tolerance 18 07 Frozen Atoms Buffered Atoms Start Write Job Files Hide Help Figure 10 1 The Constraints folder of the Impact Dynamics panel 166 FirstDiscovery 3 0 User Manual Chapter 10 Molecular Dynamics Simulations SHAKE tolerance This text box sets the tolerance for the SHAKE RATTLE algorithm The default value is 107 A for SHAKE and 107 A ps for RATTLE Increasing the tolerance will speed the calculation at the cost of allowing greater variation from the ideal values Any value greater than zero is allowed Note that the same numeric value is used for both tolerances even though the units are different 10 4 The MD Parameters Folder Use the MD Parameters folder to specify molecular dynamics settings that affect both Molecular Dynamics MD and Hybrid Monte Carlo HMC calculations see Chapter 11 Some selection options appear dimmed when they are not relevant for other previously chosen options The selection options are Integration algorithm This option menu specifies the integration algorithm employed to integrate the Equations of Motion EOM The options are Verlet and RRESPA There are no other settings to specify for the Verlet option For RRESPA three other text boxes become active as
99. csb org will have no hydrogens and may have residues in unusual charge states FirstDiscovery uses an all atom force field OPLS AA and requires correct charge states near the binding site Protein preparation for FirstDiscovery is mainly a process of neutralizing appropriate amino acid sidechains adding hydrogens orienting hydroxyl hydrogens and relieving steric clashes Protein preparation takes place in two parts After ensuring chemical correctness the preparation process neutralizes side chains that are not close to the binding cavity and do not participate in salt bridges The refinement portion performs a restrained minimization of the cocrystallized complex which reorients side chain hydroxyl groups and alleviates potential steric clashes The ProteinPrep panel allows you to specify which parts of the procedure to run Preparation and refinement Preparation only or Refinement only If you are familiar with Maestro or if you have followed Schr dinger s protein prepara tion procedure before you might need to follow only the overview provided in Section 4 3 The steps are described in detail in later sections of this chapter For a tutorial on protein preparation see the FirstDiscovery Quick Start Guide FirstDiscovery 3 0 User Manual 37 Chapter 4 Protein Preparation 4 3 Step by Step Overview This section provides an overview of the protein preparation process The procedure described assumes that the initial protein structur
100. ct A trajectory file contains a sequence of snapshots of the coordinates of the system and if requested of the velocities as well Note The Impact analysis task must be run using Impact from the command line See Chapter 3 for a brief overview of command line Impact See the FirstDiscovery Command Reference Manual available on the FirstDiscovery installation disks or on Schr dinger s support webpage http www schrodinger com Support pdf htm for additional informa tion The following two options are applicable when Record Trajectory has been selected Frames written every This text box specifies how often trajectory information is written to the trajectory file The default is every 5 MD steps Any integer value greater than zero is allowed Sample velocities This option is off by default When it is selected velocity information is written to the trajectory file FirstDiscovery 3 0 User Manual 169 Chapter 10 Molecular Dynamics Simulations 10 5 The Dynamics Folder Use the Dynamics folder to set up the type of MD simulation to be performed Options appear dimmed when they are not applicable for other options already chosen To open the Dynamics folder click the Dynamics tab of the Impact Dynamics panel The major selection options are described below The other options on this panel are described under the major option to which they apply Number of MD steps This text box sets the number of MD steps to be used
101. cted entry that precedes entry 3 To move entries to the top of the table drag them above the top of the table to move entries to the end of the table drag them below the end of the table A summary of project based mouse functions is provided in Table 2 3 16 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Table 2 3 Mouse operations in the Project Table Task Mouse Operation Change a Boolean property value Display the Entry menu for an entry Display a version of the Property menu for a property Edit the text or the value in a table cell Include an entry exclude all others Move selected entries Paste text into a table cell Resize rows or columns Select an entry deselect all others Select or include multiple entries Toggle the entry selection or inclusion state Click repeatedly in a cell to cycle through the possi ble values On Off Clear Right click anywhere in the entry If the entry is not selected it becomes the selected entry If the entry is selected the action is applied to all selected entries Right click in the column header Click in the cell and edit the text or value Click the In column of the entry Drag the entries Middle click Drag the boundary with the middle mouse button For an unselected entry click anywhere in the row except the In column for a selected entry click the row number Click the first entry then shift click the last entry Contro
102. ction by backbone picking or Residue selection by sidechain picking buttons Delete All Click Delete All to remove all residues from the OM region 8 7 3 The QM Region Ions Panel The QM Region lons panel is used to include free atoms typically ions in the QM region of a QSite job Note This option should not be used on covalently bonded atoms such as individual protein atoms and should not be used to select a subset of ligand atoms because valid QM MM cuts would not be obtained FirstDiscovery 3 0 User Manual 151 Chapter 8 QSite GM Region lons igmiormfilf ES W Show markers r B Define by picking I Basis set 6 31 G A Delete Delete All Hide Help Figure 8 7 The QM Region lons panel in QSite Click lons in the Settings folder to open the QM Region lons panel The selection options in the QM Region lons panel are QM Region Ions list The text area at the top of the panel displays the list of QM region ions as it is being constructed Show markers If this option is selected the default a set of green crosses will highlight the ions picked for the QM region Define by picking Selected by default Clicking on a free atom or ion in the Workspace adds that atom to the QM region Basis set Once an ion has been added to the OM region the basis set to be used in the calculation can be changed on a per atom basis To do so click on the ion in the ions list then select another b
103. d in the Workspace Maestro creates a scratch entry Structures that you build in the Workspace constitute a scratch entry until you save the structures as project entries The scratch entry is not saved with the project unless you explicitly incorporate it into the project However you can use a scratch entry as input for some calculations The structures and their data are represented in the Project Table which displays a list of entries Each entry is represented by a row in the Project Table Each row contains the row number an icon indicating whether the entry is displayed in the Workspace the In 12 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro column the entry title a button to open the Surfaces panel if the entry has surfaces the entry name and any entry properties The row number is not a property of the entry You can open the Project Table panel by choosing Show Table from the Project menu by clicking the Show Hide project table button on the toolbar or by pressing ALT T FER The Project Table panel contains a menu bar a toolbar and the table itself You can use entries as input for all of the computational programs Glide Impact Jaguar Liaison LigPrep MacroModel Prime QikProp and QSite You can select entries as input for the ePlayer which displays the selected structures in sequence You can also duplicate combine rename and sort entries create properties import structures as entrie
104. d is then used to determine the box center Use entry name To select an entry in the Maestro Project Table as the ligand that defines the Glide grid boxes select this button and then either type the entry name directly into the adjacent text box or use the Choose selector which displays a list of all the entries in the current opened project from which you can select an entry Use ligand from external file To define the Glide grid boxes based on a ligand in an external file select this option then use the remaining items in this panel to select a file name and structure number in that file Format Choose the format of the external file from the option menu The three file formats listed below are supported for reading in ligand files from local or network mounted disks Glide does not support Mol2 formatted files Maestro Maestro written files extensions mae out or dat MDL SD SD formatted files extensions mo1 for single structure files and sdf for multiple structure files Ligand to Define Grid ligandgrid j ej xj Specify ligand to define box center vy Use displayed ligand Q Use entry name Use ligand from external file Format Maestro Ligand file name Read Browse Structure number in ligand file 1 Hide Help Figure 6 5 The Ligand to Define Grid panel 78 FirstDiscovery 3 0 User Manual Chapter 6 Glide PDB Rutgers Center for Structural Biology Protein Data B
105. ddist Leave residue pairs forming salt bridges within idis ionized default is 3 5A Read ligand mae file ligfile Specify non default ligR mae name for output file with neutralized residues Print verbose output Minimize total charge of the receptor only Skip correction of conflicting side chain forms Leave residues within wdis of ligand ionized Set H bonding distance default 3 45 A Set cavity distance range to 8 12 A Print version number and exit Print usage message and exit FirstDiscovery 3 0 User Manual 57 Chapter 4 Protein Preparation 4 11 3 Usage Summary for impref Note impref is the driver for the refinement stage and is invoked by protprep There is little need to run impref directly Purpose To use Impact for restrained optimizations of a ligand receptor complex Syntax SSCHRODINGER utilities impref options input mae Options k 1 ligfile r rmsd s op file o1 file v h 58 Keep Impact minimization inp 1log and mae files Read ligand from file ligfile instead of input mae If this option is used input mae must be the protein structure alone If this option is not used input mae must be the protein ligand complex Specify maximum RMSD allowed default is 0 3 Write out protein and ligand separately Requires 1 ligfile Output protein or complex file Default is input_ref mae Output ligand file when s and 1 used Default is ligfile_ref ma
106. de to perform induced fit docking For more about induced fit protocols see the Prime User Manual and Prime Quick Start Guide FirstDiscovery 3 0 User Manual 69 Chapter 6 Glide 6 2 The Glide Panel Glide searches for favorable interactions between one or more typically small ligand molecules and a typically larger receptor molecule usually a protein Each ligand must be a single molecule while the receptor may include more than one molecule e g a protein and a cofactor Glide can be run in rigid or flexible docking modes In flexible docking mode Glide automatically generates conformations for each input ligand To open the Glide panel choose Glide from the Applications menu in the Maestro main menu bar The Glide panel has seven tabbed folders Settings Site Ligand Scoring Output Constraints Similarity 6 3 The Settings Folder The Settings folder defines the basic functionality of the Glide task The options in this folder determine whether the task is grid generation or ligand docking For grid genera tion this folder contains options for defining the structure in the Workspace the base name for grid files and where they will be written For docking options in this folder determine the docking mode standard precision or extra precision the number of atoms and rotatable bond thresholds for skipping ligands and which grid files to read 6 3 1 Glide Function Set Up Grids or Dock Ligands Choose
107. df for multiple structure files PDB Rutgers Center for Structural Biology Protein Data Bank files extensions pdb or ent File containing a single ligand structure When the ligand is not in the Workspace i e when Displayed structure includes the ligand is not selected the location of the ligand structure file can be entered into the Filename 124 FirstDiscovery 3 0 User Manual Chapter 7 Liaison text box Alternatively the Browse button adjacent to the text box can be used to activate the Open File panel to aid in locating the file the identity of the selected file is then displayed in the Filename text box Name to use for this ligand This text box specifies a user assigned name for the ligand The default is Lig The name is used to create a ligand directory under the Master Liaison Run Directory 7 7 The Parameters Folder The upper portion of this folder sets the Sampling method and selects options that apply to both free Ligand and bound Ligand Receptor simulations The lower portion contains sub tabs with identical features that independently control Ligand Simulation and Ligand Receptor Simulation If the Analysis folder is active you must change the Job Type setting to Simulate in the Settings folder before opening the Parameters folder 7 7 1 Sampling Method This section includes seven options two of which are dimmed when Minimization is chosen as the Sampling method Sampling method T
108. does not already exist Maestro then also creates one or more ligand directories under the Master Liaison Run Directory To open the Liaison panel choose Liaison from the Applications menu in the Maestro main menu bar FirstDiscovery 3 0 User Manual 119 Chapter 7 Liaison The Liaison panel has five tabbed folders e Settings System Parameters Constraints Analysis 7 5 The Settings Folder The Job Type option menu at the top of the folder selects Simulation or Analysis as the basic function of the Liaison task This folder also specifies the number of processors to use subject to the number of Liaison licenses in concurrent Liaison simulations on a multi processor machine A Simulation job requires additional settings in the System Parameters and Constraints folders It is usually convenient to proceed through the folders in this order but any order is allowed Liaison Host localhost 1 Settings System Parameters Constraints Analysis Job type Simulate ww Analyze results of earlier simulations Number of processors to use 1 Start Write Job Files Hide Help Figure 7 2 The Settings folder of the Liaison panel 120 FirstDiscovery 3 0 User Manual Chapter 7 Liaison The selection options in the Settings folder are Job type buttons Number of processors to use text box This section also provides instructions for killing Liaison jobs from the command li
109. e Print version number and exit Print usage message and exit FirstDiscovery 3 0 User Manual Chapter 5 Ligand Preparation 5 1 Ligand Preparation Checklist Chapter 4 discussed the preparation of receptor and ligand receptor structure files for use in FirstDiscovery Candidate ligand structures must also have certain characteristics for FirstDiscovery applications Some of these conditions can be met by using Maestro features or command line utilities to alter the ligand structure file To be submitted to Glide and other applications ligand structures 1 Must be three dimensional 3D 2 Must each consist of a single molecule that has no covalent bonds to the receptor with no accompanying fragments such as counter ions and solvent molecules 3 Must be in a Maestro format file Maestro transparently converts SD MacroModel and PDB formats to Maestro format during structure import Maestro also transpar ently converts Mol2 during import However FirstDiscovery has no direct Mol2 sup port so make sure your structures are in Maestro SD or PDB format before beginning FirstDiscovery jobs Structure file format conversion can be done from the command line using utilities such as pdbconvert sdconvert and maemmod See the Maestro User Manual 4 Must have all their hydrogens filled valences These can be added in Maestro by using either the Add hydrogens toolbar button H or the Hydrogen Treatment panel select
110. e ieu FirstDiscovery 3 0 User Manual F Fast Multipole Method FMM 140 156 157 163 hierarchy level setting and RRESPA file IO directory see file names in FirstDiscovery 28 file par teter nocet catene 154 filtefs eene 15 16 hierarchical eene 86 final scoring s sa 89 five and six membered rings 83 fixed entries uenire reete 16 flags Ja gaf ccein niisiis 148 flexible docking 66 68 83 flexible ligands ese 66 flexible receptor docking 73 force field 28 154 OSite C 140 format conversion to Maestro 59 format Mol2 ssssssssseeeeeereeen 81 fragments building structures with 18 tree ligands ener 154 free ligands selection 150 free ligands selection mode 151 frozen atoms in Impact constraints 161 frozen atom constraints 142 160 OTi RE 142 160 G generate conformations eeeee 83 Glide Active Site Residues panel conformational search Constraints folder described 4 uoc esin distributed processing Dock Displayed Ligand
111. e Clicking this button alters Contact Set 1 as listed in the Contacts folder to be the receptor molecule or molecules and Contact Set 2 to be all other molecules This action also displays the contact markers The contact settings can be viewed and altered using controls in the Contacts folder which can be opened either from the Glide Pose Viewer Panel or from the Measurements panel on Maestro s main menu bar Write Displayed Poses This button is enabled only when the receptor or at least one of the ligand pose structures is displayed in the Workspace This button opens the PoseWrite panel which enables displayed pose structures to be written out to another file The operation of the PoseWrite panel is described in Section 6 10 2 H Bonds Folder This folder contains controls that set the criteria for display of hydrogen bonds The H Bond controls in this folder operate in the same way as those in the H Bonds folder in the Maestro Measurements panel See the Maestro User Manual or the Maestro online help for more information Contacts Folder The controls in this folder set the criteria for display of contacts Contacts can be good bad or ugly Any combination can be shown or hidden by using the Mark Contacts buttons Good contacts are displayed as green bad contacts as orange and ugly contacts as red The controls in this folder operate in the same way as those in the Contacts folder in the Measurements panel See the Maestro
112. e Note that tabs cannot be used to sepa rate the ligand names though spaces can Name of Ligand Binding Energy File This option is available for the Fit task It requires a text file containing a list of ligand names and associated binding energies The ligand binding energies should be in kcal mol to match the output of the Liaison calculation other choices such as kJ mol or pK will give correct numerical results in the same units but kcal mol will still be printed You would create a text file like that shown below Note that the minimum number of ligands is 3 as there are 3 LRM parameters to fit In actual practice binding energies of at least 7 and ideally of 10 or 20 or more ligands should be fit 1bkm 3m 1 50 0 5 l1bkm 3m 2 10 9 l1bkm 3m 3 211 9 The first column contains the user defined ligand names while the second lists the experi mental binding affinities Each name in the first column must correspond to a directory under the Master Liaison Run Directory See the preceding discussion under File Name Note that only spaces can be used to separate the ligand names and binding energies FirstDiscovery 3 0 User Manual 135 Chapter 7 Liaison 7 10 Running Liaison as a Stand Alone Program You can run Liaison simulations from a terminal window by using and editing if desired files written by Maestro when you select Write Job Files from the lower portion of the Liaison panel Alternatively you can set up the direc
113. e field Sort poses based on model energy score Emodel Overrides use of dock ing score field Don t sort the poses Retain only the nreport lowest scoring poses Don t include the receptor structure in output files Keep only the single best pose for each ligand in each input pose file Keep only the single best pose for each ligand with a given lignum value Keep only the single best pose for each ligand with a given title Print help message and quit Print version number and quit FirstDiscovery 3 0 User Manual Chapter 6 Glide Custom Scoring Function Options Setting any of these custom scoring function terms causes glide sort to sort only on this custom function instead of the standard use sorting options gscore coef GlideScore coefficient default 0 0 for custom scoring function cvdw coef E CvdW coefficient default 0 0 for custom scoring function internal coef E internal coefficient default 0 0 for custom scoring function emodel coef Emodel coefficient default 0 0 for custom scoring function offset coef Energy offset default 0 0 for custom scoring function Filter Options hbond cut cutoff Filter cutoff for H bond energy default 0 0 cvdw cut cutoff Filter cutoff for E Cvdw default 0 0 metal cut cutoff Filter cutoff for metal ligation energy default 0 0 emodel cut cutoff Filter cutoff for Emodel not used by default nofilter Don t use filter cutoffs at all
114. e stereoizer 10 Generate low energy ring conformations When ring conformation information is not available it is important to generate a range of conformers so that the low energy structures can be located Ring confir mations are generated for each structure by ring_conf 11 Remove problematic structures Structures that could cause subsequent processing failures either in the energy mini mization of the structures or in other applications are removed by premin 12 Optimize the geometries The geometries of the generated structures are optimized using a restricted version of the MacroModel computational program bmin or a short conformational search is performed to relax the structure into 3 dimensions while strongly encouraging chiral centers to adopt the proper chiralities if the structure is highly strained FirstDiscovery 3 0 User Manual 61 Chapter 5 Ligand Preparation 13 Convert output file If output in SD format was requested sdconvert is run to perform the conversion 5 2 2 The LigPrep Panel The LigPrep panel allows you to set up LigPrep jobs in Maestro Choose LigPrep from the Applications menu to open the panel For details of panel options and operation see the LigPrep User Manual Below are notes on panel options that produce more than one output structure per input structure The default options in the LigPrep panel run the desalter add hydrogens and minimize the ligand structure performing a
115. e All Hide Help Figure 6 6 The Active Site Residues panel FirstDiscovery 3 0 User Manual 79 Chapter 6 Glide Define active site residues The picking controls in this section of the panel allow you to select the residues that constitute the active site For more information about picking controls and the Atom Selec tion dialog box ASD see Section 2 6 on page 21 search for picking controls in the Maestro online help or see the Maestro User Manual 6 5 The Ligand Folder The Glide Ligand folder allows you to identify the ligands to be docked or scored by Glide You can also specify a reference ligand for use in rms comparisons of docking accuracy 6 5 1 Ligand Folder Features Dock displayed ligand When this button is on the ligand currently displayed in the Workspace will be docked by Glide This option is enabled only when the ligand molecule has been identified in the Workspace see the Displayed structure is option menu in the Settings folder in Section 6 3 3 on page 72 Dock displayed ligand only If you have selected Dock displayed ligand this option becomes available Choose it if you do not want to dock any ligands from the Project Table or external files Dock selected entries from project table This button indicates that Glide should dock all the entries selected in the Project Table This can be done instead of docking ligands from external files but with or without docking the disp
116. e default for this base penalty is 6 0 but any real value is allowed A value of 0 0 is equivalent to running without FirstDiscovery 3 0 User Manual 101 Chapter 6 Glide similarity scoring and negative values result in rewards rather than penalties for ligands that are dissimilar to the compounds in the actives file Fully penalize ligands with similarity lt ____ The value entered here is the similarity threshold Smin below which ligands get the full penalty or reward This is a real number between 0 0 and 1 0 with a default of 0 3 and must be less than or equal to the Zero Penalty threshold in the next item Note that it is always the maximum similarity of a ligand to any active compound that determines its GlideScore adjustment whether that adjustment is a penalty or a reward for dissimilarity Glide glide Job glidetmp Login dya11 Host localhost 1 Settings Site Ligand Scoring output Constraints Similarity i H Format Filename of known actives Chog e Formak Filename of knoven inar tives Percentage of inactives fo keeps 10 Yo W Use similarity score in docking Choose Format Maestro Filename of known actives Choose Ce _ Weight similarity scores using file wgt Base penalty value 6 00 kcal mol Fully penalize ligands with similarity 0 30 No penalty for ligands with similarity gt o 70 Reject ligands with similarity lt o o
117. e following prep Preparation only refine Refinement only both Preparation and refinement default Print verbose debugging output Run the job on a remote host Run the job in the current directory rather than in a temporary scratch directory Keep job in foreground Do not return until the job completes The default is to run protprep in the background Run the job at reduced priority Print usage message and exit Minimize total charge of receptor only Skip correction of conflicting side chain forms Set cavity distance range to 8 12 A Suitable for Liaison jobs Leave residue pairs forming salt bridges within dist A ionized default is 3 5 A Leave residues within dist A of ligand ionized Set H bonding distance default is 3 45 A FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation Refinement Stage Options rmsd keep separate Maximum RMSD allowed for refinement default 0 3 Keep intermediate structure files Write out refined protein and ligand structures sepa rately rather than in one combined structure 4 11 2 Usage Summary for pprep Note pprep is the driver for the preparation stage and is invoked by protprep There is little need to run pprep directly Purpose To adjust protonation states of a receptor in a Maestro format file Syntax SCHRODINGER utilities pprep options proteinfile mae Options E i idis ligfile outfile wdis hbon
118. e is in a PDB format file includes a cocrystallized ligand and does not include explicit hydrogens For best results structures with missing residues near the active site should be repaired before protein preparation After processing with Schr dinger s protein preparation facility you will have files containing refined hydrogenated structures of the ligand and the ligand receptor complex The prepared structures are suitable for use with any FirstDiscovery application In most cases not all of the steps outlined need to be performed See the descriptions of each step to determine whether it is required 1 Import a ligand protein cocrystallized structure typically from PDB into Maestro 2 Locate any waters you want to keep then delete all others Generally all waters except those coordinated to metals are deleted but waters that bridge between the ligand and the protein are sometimes retained 3 Simplify multimeric complexes Determine whether the protein ligand complex is a dimer or other multimer containing duplicate binding sites and duplicate chains that are redundant If the structure is a multimer with duplicate binding sites remove redundant binding sites and the associated duplicate chains by picking and deleting mole cules or chains in Maestro 4 Adjust the protein metal ions and cofactors Fix any serious errors in the protein Incomplete residues are the most common errors but are relatively harmless if t
119. e numbers of ligands are to be studied Those predicted to be most active might then be re examined using a simulation protocol HMC is recommended if desired 7 3 Liaison Analysis A Liaison analysis calculation uses the results of completed Liaison simulations to fit the binding energy model coefficients to the binding energies of known ligands or to predict the binding energies of new ligands To use the results of earlier simulations a Liaison Analysis job must be run from the same directory Maestro working directory and the same text string must be entered into the Job text box to identify the Master Liaison Run Directory In addition the supplied ligand names must be the same as those used in the simulation calculations 7 3 1 Fitting the Simulation Results to Experimental Data A Liaison fitting calculation requires a text file containing a list of the ligand names and their associated experimental binding energies This text file can reside in any directory The format is LigandName space BindingEnergy Example Ligand1 7 32 Ligand2 7 73 Ligand3 9 20 118 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Ligand4 8 06 Ligand5 10 01 The ligand names must be the same as those used in the preceding Liaison simulation calculations Units of kcal mol are assumed If other units are employed kJ mol pK or IC 9 the numerical results are correct in those units but kcal mol is still printed Before s
120. e panel The merged entry should be the only entry included in the Workspace when you start the job One exception to this is when setting up a transition state search In this case you may select up to three Project Table entries depending upon the algorithm that is selected for performing the search See Section 8 6 on page 144 for more information about transition state searching The default job name for a QSite job is qsitetmp QSite jobs can be monitored in the job Monitor panel However if a QSite job needs to be restarted it must be restarted from the command line To restart a QSite job 1 Rename the jobname out mae file to jobname mae 2 Rename the jobname jaguar 01 in file to jobname jaguar in FirstDiscovery 3 0 User Manual 139 Chapter 8 QSite 3 Restart the job using the command impact ijobname inp j jobname jaguar in 8 2 The QSite Panel To open the QSite panel choose QSite from the Applications menu The QSite panel has five tabbed folders used as follows Potential choose settings for the MM potential energy function Constraints set up atom constraints for atoms in the MM and QM regions Minimization set up energy minimization of the MM region Optimization select and set up the job task single point energy calculation geome try optimization or transition state search QM Settings specify the QM region and other QM options 8 3 The Potential Folder The first three QS
121. eature allows large libraries to be screened at an affordable computational cost 6 1 1 Glide Constraints A Glide constraint is a ligand receptor interaction requirement To use Glide constraints specify up to ten receptor sites for possible ligand interactions when you set up a grid 68 FirstDiscovery 3 0 User Manual Chapter 6 Glide generation job When you run a docking job you can select up to four Glide constraints to apply from the list of receptor constraint sites you defined for that receptor In Glide constraint docking jobs Glide incorporates satisfaction of these constraints into several of its hierarchical filters allowing prompt rejection of docked poses that fail to meet the requirements This can significantly speed up docking improve database enrich ment and in some cases increase docking accuracy For information on using Glide constraints see Section 6 8 on page 94 See the FirstDis covery Technical Notes for details about the method and for a discussion of results 6 1 2 Glide Extra Precision Mode The extra precision XP mode of Glide combines a powerful sampling protocol with the use of a custom scoring function designed to identify ligand poses that would be expected to have unfavorable energies based on well known principles of physical chemistry The presumption is that only active compounds will have available poses that avoid these penalties while at the same time securing a favorable scoring from the ter
122. eceptor atom chosen is identified by atom number atom type residue type and number chain Symmetry equivalent atoms defined by a single constraint are separated by commas within square brackets Pick to choose atoms This option is selected by default allowing you to define possible Glide constraints by picking atoms in the receptor Show markers Selected by default this option marks the receptor constraint sites you select with red crosses and padlocks Up to ten symmetry distinct receptor atoms can be chosen as possible constraint sites though no more than four constraints may be applied for a given docking job Typically these are receptor atoms that are known to be important in binding from structural or biochemical data But they can be any receptor atom capable of forming a hydrogen bond with the ligand or any metal ion included in the receptor In the case of a hydrogen bonding interaction the receptor atom must be a polar hydrogen nitrogen or oxygen If you choose an atom with one or more symmetry equiva lent atoms in its functional group the symmetry equivalent atoms will all be selected as well and collectively count as one constraint For example if you create a constraint by picking one oxygen atom of a carboxylate group Glide includes the other oxygen atom in the same constraint A ligand interaction with either oxygen atom will satisfy that single constraint In the case of a metal ligand interaction constraint
123. ecule If you chose Receptor plus a single ligand from the Displayed structure is option menu then this picking button becomes active When the button is active the ligand molecule can be identified by picking any atom in the ligand displayed in the Workspace The ligand molecule will then be marked with dark green markers If you chose Ligand alone from the Displayed structure is option menu Maestro automatically identifies the ligand For Glide to operate correctly you must identify the ligand if it is present in the Workspace Skip ligands with gt n atoms Use this text box to set the maximum number of atoms for a ligand structure to be docked Ligand structures in the input file with more than the specified number of atoms will be skipped The default is 100 atoms This maximum number of ligand atoms can also be used in the Site folder to calculate the size of the enclosing box for the grids This number should be reduced if the active site region is small and enclosed to speed up a docking calculation on a large ligand database Skip ligands with gt n rotatable bonds Use this text box to set the maximum number of rotatable bonds a ligand structure may have if it is to be docked Ligand structures in the input file with more than this number of rotatable bonds will be skipped The default is 15 rotatable bonds This number should be reduced if you want only relatively small or rigid ligand hits Base name for grid files This text bo
124. ed the result will be to buffer atoms between 8 and 12 from the nearest atom in the ligand and to freeze atoms greater than 12 away Note These buffered atom selections are keyed to the Workspace structure that you see on screen Jobs will only include these constraints if they are run on the Workspace structure FirstDiscovery 3 0 User Manual 131 Chapter 7 Liaison 7 9 The Analysis Folder The following analysis jobs are available Determine binding energy model coefficients by fitting to known binding energies Fit Apply supplied binding model equation coefficients to predict binding energies for new ligands Predict In either case the Simulate task selected in the Settings folder must first be used to complete the requisite Liaison runs Before an Analysis job can be run the following conditions must be met Maestro must be in the same directory Maestro working directory that was used when the simulation calculations were run You can ensure Maestro is in the correct directory by starting Maestro in the same directory that was used when the simulation calculations were run the Maestro working directory or by executing the changedir command in Maestro s com mand input area to change to the Maestro working directory The Master Liaison Run Directory must be correctly identified You can do this by entering the jobname string used in the preceding Liaison simu lations in the Job text box at the top of
125. een the reactant and the product If you want to pick a guess structure closer to the reactant move this slider between 0 00 and 0 50 For a guess structure closer to the product select a value between 0 50 and 1 00 8 7 The QM Settings Folder The QM Settings folder is used to enter information for the QM job and to define the QM region QM job information includes the quantum mechanical method to be used the charge and spin multiplicity of the QM system the number of processors if Jaguar parallel processing is available and other keywords and options that may be required by Jaguar The QM region can be defined by Selecting the ligand metal ions or other disconnected species not covalently bonded to the protein Specifying cuts between certain covalently bonded atoms in connected residues QSite cuts are specially parameterized frozen orbital boundaries between the QM and MM regions 8 7 1 QM Settings Folder Features Method The options for QM method are Density Functional Theory DFT B3LYP Hartree Fock and Local Mgller Plessett perturbation theory Local MP2 Charge Multiplicity The Charge text box should contain the net charge of the QM region of the system and the Multiplicity text box should contain the associated spin 1 for singlet 2 for doublet and so on Maestro updates the Charge text box with reasonable entries whenever a new residue or ion is added to the QM region However both the Charge and Mu
126. el on the main toolbar 3 In the Atom Properties folder of the Build panel choose Atom Type MacroModel from the Property option menu 4 Find the correct atom type for the mistyped atom and click it in the list 5 Click on the atom to be changed 4 8 2 Manually Deleting Explicit Ligand Metal Bonds If the complex structure contains any bonds from the ligand or a cofactor to a protein metal they must be deleted Glide and the OPLS AA force field it uses models such interactions as a van der Waals plus electrostatic interaction Glide cannot handle normal covalent bonds to the ligand such as might be found in an acyl enzyme Maestro will delete all bonds to metal atoms before the protein preparation job begins However if there are metal ligand bonds they will interfere with the identification of the ligand molecule To avoid this delete such bonds manually 1 To check for ligand metal bonds you can use Maestro s Display Undisplay facility a On the toolbar choose Protein Backbone from the Undisplay button menu lt a EI b Repeat the process choosing Protein Side Chains 2 If any metal ligand bonds exist delete them a Choose Bonds from the Delete button menu on the toolbar b Click on the bonds to be deleted 3 Redisplay the complete protein by choosing All from the Display Only button menu on the toolbar 50 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation 4 8 3 Checking for Other Protein Li
127. elect this button and then either type the entry name directly into the adjacent text box or use the Choose selector which displays a list of all the entries in the current opened project from which you can select an entry Use ligand from external file Format The three file formats listed below are supported for reading in ligand files from local or network mounted disks Glide does not support Mol2 formatted files Maestro Maestro written files extensions mae out or dat e MDL SD SD formatted files extensions mo1 for single structure files and sdf for multiple structure files PDB Rutgers Center for Structural Biology Protein Data Bank files extensions pdb or ent Ligand file name Specify the name of the file in which to find the reference ligand The Browse but ton to the right of the text box can be used to locate the file Structure number in ligand file If the ligand file contains multiple structures you can specify the structure to be read as the reference ligand by entering the structure number of the ligand in the file 6 6 The Scoring Folder The settings in the Scoring folder define the manner in which Glide processes the ligand poses i e combinations of position orientation and conformation it generates These poses pass through a series of hierarchical filters that evaluate the interaction of the ligand with the receptor Stages 1 and 2 see Figure 6 2 on page 67 test the spatial fit o
128. els in Maestro only one Impact panel can be open at a time If you choose an item from the Impact menu while another panel is open the existing panel is dismissed before the new one is displayed Help Opens the Help panel with an appropriate help topic displayed 4 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Maestro is the graphical user interface for all of Schr dinger s products FirstDis covery Glide Impact Liaison and QSite Jaguar LigPrep MacroModel Prime and QikProp It contains tools for building displaying and manipulating chem ical structures for organizing loading and storing these structures and associated data and for setting up monitoring and visualizing the results of calculations on these struc tures This chapter provides a brief introduction to Maestro and some of its capabilities For more information see the Maestro User Manual 2 4 General Interface Behavior Most Maestro panels are amodal more than one panel can be open at a time and a panel need not be closed for an action to be carried out Instead of a Close menu option or button each Maestro panel has a Hide button so that you can hide the panel from view Maestro supports the mouse functions common to many graphical user interfaces The left button is used for selecting choosing menu items clicking buttons and selecting objects This button is also used for resizing and moving panels The right
129. emotely make sure the job files are accessible from the remote machine 7 2 2 Directories Created Master Liaison Run Directory This directory is created by Maestro under the Maestro working directory on starting the job or writing job files The Master Liaison Run Directory name is defined by the text entered in the Job text box in the top left corner of the Liaison panel Hence jobname Master Liaison Run Directory Your choice for the Job text string is denoted as jobname The Master Liaison Run Directory specifies a relative rather than an absolute path 114 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Liaison Directory Structure Maestro Working Directory Master Liaison Run Directory jobname ligandl ligand2 ligand3 ligand4 Input Output analyze Jjobname 44 simulate jobname jobname dat jobname in jobname 1og jobname mae jobname out change sgbparam jobname ligand5 ligand stdout ligand2 stdout ligand3 stdout ligand4 stdout ligand5 stdout jobname 1og ligand _structure ligand _lig_min mae receptor_structure ligand _rec_min mae ligand ree inp ligand free out ave amp log ligand bound inp ligand bound out ave amp log ligand lig fin mae ligand rec fin mae ligand bound trj cmpx rst ligand ree j Figure 7 1 The Liaison directory structure Files in brackets are created only with Lia
130. en in the HMC or Dynamics sections The table below shows how the conversion is made Task Conversion Formula HMC Heating Time 2mxcyc nmdmc delt 6 MD Heating Time nstep delt 6 Min N A Liaison Minimization jobs do not do heating at all FirstDiscovery 3 0 User Manual 127 Chapter 7 Liaison mxcyc of HMC cycles nmdmc of MD steps per MC cycle nstep of MD steps delt time step in ps delt is 0 002 ps for HMC and 0 001 ps for MD The default 0 002 ps time step for HMC and 0 001 ps time step used for Liaison dynamics MD jobs cannot be modified in Maestro but can be edited by hand in the input files However this is not recommended The factor of 6 comes from the fact that heating is broken up into six equal stages Example HMC method Heating time 15 ps Resultant input file HMC section only HMC input cntl mxcyc 83 nmdmc 5 delt 0 002 relax 0 01 nprnt 100 seed 101 The number of HMC steps mxcyc is five times smaller than the number of MD steps nstep because each composite HMC step includes five MD steps set by nmdmc 5 in the example above Note also that the calculated number of steps 83 corresponds to one sixth of the requested heating time This is because Liaison heats the ligand protein complex but not the free ligand in six equal temperature increments each of which receives one sixth of the total heating time For example for a target temperature of 300 K the heating is done in 50
131. en you set up a docking job using the grids you have generated the Glide constraint sites associated with those grids appear in the Receptor constraint sites list in the Glide Constraints folder For any single docking job you can select up to four Glide constraints Each site you select will be required to interact with the ligand during docking Select from one to four sites for constraints by clicking on them to highlight them To deselect a constraint click it again If there are no constraints selected when you start the docking job no constraints will be applied Multiple docking jobs can be run using the same receptor grids but choosing different subsets of the defined Glide constraints Note Grid files containing Glide constraint definitions that were generated in FirstDis covery versions earlier than 3 0 will still work in FirstDiscovery 3 0 but you will not be able to use the subset feature You can use all of the constraints the default or use none of 94 FirstDiscovery 3 0 User Manual Chapter 6 Glide them The latter option requires you to edit the input file See the FirstDiscovery Release Notes for instructions 6 8 2 Glide Constraints Folder Features Grid Generation When the Glide task chosen in the Settings folder is Set up grids the following features appear in the Constraints folder Receptor constraint sites This list remains empty until you have selected a site in the receptor for a Glide constraint Each r
132. energy ring conformations rings per ligand Desalt is selected by default 62 FirstDiscovery 3 0 User Manual Chapter 5 Ligand Preparation Generate tautomers is selected by default The tautomerizer generates up to 8 tautomers per ligand selecting the most likely tautomers if more than 8 are possible If you are comfortable that the input structures are already in the correct tautomeric form for docking to a particular target then the tautomerizer should be turned off by deselecting Generate tautomers 5 3 The Ionization State Expander ionizer While LigPrep as a whole requires additional licenses one LigPrep tool the ionizer is included with FirstDiscovery This section provides an introduction and usage summary for the ionizer as a service in FirstDiscovery The ionizer generates ionization states of ligands to match the pH range and other conditions you specify The resulting ligands can be used as input to programs such as Glide Starting with a Maestro format input file of neutral molecular structures for example from a database the ionizer produces a Maestro format output file that has expanded to include multiple ionization states of each molecule allowing Glide to select among them The ionizer requires the installation of a module called services When you run the INSTALL script to install Schr dinger software be sure to select the services product which contains the ionizer software For more information on inst
133. eparate entries This setting determines how the output structure is included in the Maestro Project Table upon job completion Separate entries returns the protein and ligand as sepa rate entries whereas Single entry does not Single entry may be more convenient if you want to run calculations on the complex with the existing ligand immediately 4 9 5 Launching the ProteinPrep Job To launch a ProteinPrep job click Start The monitor panel is displayed and the results of the job are shown If you decide to run preparation and refinement separately you will need to run a Preparation only job and refine the results with a subsequent Refinement only job If you want to run the job from the command line click Write Files See Section 4 11 on page 55 for information on command line options 4 9 6 Output Job Files Running Preparation and refinement produces the same files as running Preparation only followed by Refinement only The following structure files are produced where struct is the name of the complex struct_lig mae The input ligand structure file struct_lig_prep mae The post preparation ligand structure file FirstDiscovery 3 0 User Manual 53 Chapter 4 Protein Preparation struct_lig_ref mae The post refinement ligand structure file struct_prot mae The input receptor structure file struct_prot_prep mae The post preparation receptor structure file struct prot ref mae The post refinement receptor and ligand structures st
134. er amide bond rotations are to be penalized and whether ring conformation flips will be allowed Score in place options include whether to count amide bonds as rotatable Generate conformations for each input structure flexible docking This option directs Glide to generate conformations internally during the docking process a procedure known as flexible docking At present conformation generation is limited to variation around acyclic torsion bonds generation of conformers for five and six membered rings and generation of pyramidalizations at certain trigonal nitrogen centers e g in sulfonamides To carry out more complete conformational exploration you would have to explicitly include in the input ligand file a representative structure for each larger ring conformation believed to be relevant When flexible docking is selected the amide and ring conformation options are Penalize amide bond rotations SP freeze XP restrain to cis trans The default is not to penalize amide bond rotations In SP default docking selecting this option freezes amide bonds in their input con formation throughout docking no rotations will occur FirstDiscovery 3 0 User Manual 83 Chapter 6 Glide In extra precision XP docking selecting this option does not prevent cis to trans or trans to cis conformation changes but non planar amide bonds are heavily penalized Allow ring flips The default is to allow ring flips Deselect this
135. er is the only option selected e Click on an atom of the ligand The ligand s molecule number is shown 2 In the Commands text box enter displayonlyatom fillres within dist mol num molnumlig where molnumlig is the molecule number determined in Step 1 This will display the ligand plus all atoms including water oxygens within the chosen distance dist A of the ligand The display of whole residues with any atoms within the chosen distance can also be accomplished using the Atom Selection dialog box ASD For more informa tion see the online help or the Maestro User Manual 3 To visualize the resulting waters a From the Display menu choose Molecular Representation b In the Atoms folder choose the Representation option Ball amp Stick c Click Select to open the ASD d In the Residue folder select Residue Type 40 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation e Click the water residue type HOH f Click Add g Click OK The water oxygens assuming no hydrogens have been added are displayed in ball and stick representation as balls Alternatively you can enter repatom rep ballnstick res HOH in the Commands text box 4 5 2 Should Structural Waters Be Kept Keeping structural waters is likely to be more important for Liaison than for Glide Deleting all waters to make a site more accessible might be desirable in a Glide project For example retaining the water under the flap in 1HP
136. er than or equal to zero K 172 FirstDiscovery 3 0 User Manual Chapter 11 Hybrid Monte Carlo Simulations 11 1 Using the Hybrid Monte Carlo Panel Use the Impact Hybrid Monte Carlo panel to set up and run a Hybrid Monte Carlo HMC simulation on the Workspace structure HMC simulations achieve relatively efficient sampling by interleaving Monte Carlo moves with a short sequence of molecular dynamics steps Because HMC is used mainly as a sampling method for example in Liaison binding affinity calculations the MD steps can use a somewhat larger time step than would normally be advisable The Metropolis algorithm determines which MC moves should be accepted or rejected This ensures that the simulation does not go far astray even if the MD time step would normally lead to a failure of energy conservation this is why HMC is sometimes called bad MD but good MC To open the Impact Hybrid Monte Carlo panel Inthe Maestro Applications menu choose Hybrid MC from the Impact submenu In the upper part of the panel are the standard FirstDiscovery panel options for Job name Login and Host as well as Source of job input and Incorporate output into project by For a description of these options see Section 1 2 The default job name for Impact Hybrid MC jobs is impacttmp The input for an Impact Hybrid MC job can be either the contents of the Workspace or a single entry in the Project Table To perform Hybrid Monte Carlo simulation
137. es Hide Help Figure 8 1 The Potential folder of the QSite panel Use distance based cutoffs Select this option previously Use truncation to truncate nonbonded interactions For more information see Section 9 4 3 on page 157 There are two settings which can be changed Update neighbor list frequency Choose the number of steps after which the neighbor list will be updated The default is 10 steps e Residue based cutoff distance All atoms within complete residues which have any pair of atoms within this distance will be included in the nonbonded interaction list The default is 12 A Use continuum solvation This option affects both MM and QM calculations Do not select Use continuum solvation if you would like to run the QM Jaguar calculation using multiple processors parallel processing when QSite jobs with solvation are run in parallel erroneous energies result For more information about continuum solvation options see Section 9 4 6 The only available solvation method in QSite for both the MM and the QM solvation functions is the Poisson Boltzmann Solver PBF selecting Use continuum solvation FirstDiscovery 3 0 User Manual 141 Chapter 8 QSite automatically sets both solvation functions to PBF in the Jaguar input file isolv 2 The following settings can be changed Resolution The Poisson Boltzmann solver involves a finite element calculation on a grid The grid spacing controls the
138. es typically end in _pv mae The File text box is read only file names cannot be directly entered there Receptor Display The first structure in the pose file is assumed to be the receptor The receptor can be displayed or undisplayed by toggling the Display button Note that this action affects the numbering of the molecules in the Workspace In particular the initial Pose Viewer display will have the receptor as molecule 1 or 1 to n if it is composed of n molecules and the displayed ligand pose as molecule 2 or n 1 When the receptor is undisplayed the displayed ligand becomes molecule 1 and remains molecule 1 when the receptor is redisplayed This change in numbering affects ASL commands that you might want to employ to restrict the Workspace display to the region of the receptor near the ligand to color certain species in certain ways or for some other purpose see the Maestro User Manual or Maestro online help for information on ASL expressions Note however that when the next ligand is displayed the protein will again become molecule 1 or 1 to n while the new ligand will be molecule 2 or n 1 FirstDiscovery 3 0 User Manual 103 Glide Chapter 6 jaund 1 M 1 A esog IYI fo 42pjof sasod IYL FI 9 294n314 snolAad e ej es t es ves fore eat S 2 LH s ve ejere forse ese esej si e BL CH wt L1 9 e eae 237 sse esei sef Pe ZO OL of af sse fe ee osss Jzze e
139. f the ligand to the defined active site and examine the complementarity of ligand receptor interactions using a grid based method patterned after the empirical ChemScore function Eldridge et al J Comput Aided Mol Des 1997 11 425 445 Poses that pass these initial screens enter the final stage of the algorithm which involves evaluation and minimi zation of a grid approximation to the OPLS AA nonbonded ligand receptor interaction energy Final scoring which by default uses Schr dinger s proprietary GlideScore multi ligand scoring function is then carried out on the energy minimized poses Finally if GlideScore 86 FirstDiscovery 3 0 User Manual Chapter 6 Glide was selected as the scoring function a composite Emodel score is used to rank the poses and to select the pose or poses to be reported to you Emodel combines GlideScore the nonbonded interaction energy and for flexible docking the excess internal energy of the generated ligand conformation There are three main sections in the Scoring folder Refinement of initial poses on coarse grid Energy Minimization Final Scoring Glide glide Job dock_confgen Login saunders Host localhost 1 settings site Ligand Scoring output Constraints simitarity Refinement of initial poses on coarse grid Keep 5000 initial poses per ligand for refinement Scoring window for keeping initial poses 100 0 Keep 400 refined poses per liga
140. f the file or select the file in the Files list Click Import na A N To display the Project Table click the Show Hide project table button on the toolbar EH The imported entry is highlighted in the Project Table and visible in the Workspace 4 5 Deleting Unwanted Waters Water molecules in the crystallographic complex are generally not used unless they are judged critical to the functioning of the protein ligand interaction When waters are used they are later included in the protein as structural waters If you know there are no waters that are important to the protein ligand interaction skip to Section 4 5 3 to delete all waters FirstDiscovery 3 0 User Manual 39 Chapter 4 Protein Preparation 4 5 1 Locating Structural Waters To probe for structural waters in the protein structure 1 Locate the ligand and determine its molecule number The ligand is usually evident when PDB structures are imported into Maestro because structures that are not standard amino acid residues are colored orange while complete standard residues are gray If the ligand is not evident a On the toolbar choose Chain Name or Molecule Number from the Color all atoms by scheme button menu amp Locate the ligand b From the Display menu choose Atom Labels The Atom Labels panel opens c Make sure the selected Mode is Add and the Label Atoms pick state is Atoms d In the Composition folder make sure that Molecule Numb
141. file or for PDB files is generated from the file name The ligand number conformation number and pose number are also shown The G Score GlideScore Emodel and Energy values calculated by Glide are shown whenever they are available The Hbond Good vdW Bad vdW and Ugly vdW values shown are the numbers of H bonds and contacts between the posed ligand and the receptor evaluated by Maestro according to the current H bond and contact measure ment criteria Selection of Ligand Poses A single ligand pose can be selected and displayed by clicking on its entry row Additional entries can be added to the selection and to the Workspace display by holding down either CTRL or SHIFT and clicking on their entry rows This might be done to visualize two or more poses simultaneously or to select a subset of poses to write to an external file using the Write Displayed Poses button Control click acts as a toggle and thus can be used either to add a new entry to the Workspace or to de select an existing entry Unlike some other selection paradigms the Pose Viewer does not allow a range of entry rows to be added to the selection via a single shift click Modifications in the Workspace Modifications of selected Pose Viewer structures affect only the Workspace For example if a pose is selected in the Pose Viewer modified in the Workspace say some atoms are deleted unselected in the Pose Viewer and then reselected the pose will be displayed in i
142. file to be written to a different file name than jobname 1og you can designate a specific file name with o logfile For distributed processing the xun jobs p1 script can be used Distributed processing for Basic Impact calculations is not available from the GUI 3 4 6 Using Job Control Commands Once your jobs are launched you can monitor their progress using the Monitor panel in Maestro The command SCHRODINGER jobcontrol can also be used It has many options but the two most useful options are SSCHRODINGER jobcontrol list which will show the status of all your jobs and SSCHRODINGER jobcontrol kill to terminate any job and its subjobs if any exist For a summary of jobcontrol options use SSCHRODINGER jobcontrol h For more information see the Maestro User Manual For an introduction to running and monitoring jobs in Maestro see Section 2 10 on page 24 34 FirstDiscovery 3 0 User Manual Chapter 3 FirstDiscovery from the Command Line 3 5 Using Command Line Utilities Several FirstDiscovery support modules are command line applications or utilities struc ture preparation utilities and applications structure conversion utilities and Glide utilities The command line application protprep is located in the main Schr dinger directory Utilities are located in the directory SCHROI DINGI ER utilities You may want to add this directory to your path so that they are easy to run by
143. for the simulation The default setting is 100 steps but any number greater than zero is allowed Time step This text box sets the time step for the MD simulation The default value is 0 001 ps but any value greater than zero is allowed A somewhat larger value 0 0015 or 0 002 may be suitable if bond lengths are constrained see the Impact Constraints folder in Section 9 5 on page 160 or if the RRESPA integrator is employed see the MD Parameters folder in Section 10 4 on page 167 Impact Dynamics idynamics Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by amp ppending new entries Replacing existing entries Do not incorporate Potential Constraints MD Parameters Dynamics Number of MD steps 100 Time step ps 0 001 Ensemble type Constant pressure NPT Target temperature K 298 15 Temperature relaxation time ps 0 01 Target pressure atm 1 Volume relaxation time ps 0 01 Solvent isothermal compressability 4 96e 05 Effective density 1 Volume scaling Molecule center of mass W Initialize velocities fram Gaussian distribution Initial temperature K 298 15 Start Write Job Files Hide Help Figure 10 3 The Dynamics folder of the Impact Dynamics panel 170 FirstDiscovery 3 0 User Manual Chapter 10 Molecular Dynamics Simulations Ensemble
144. g input files S Split input ligand file by subjob 0 Have log file written directly to output directory only meaningful if x option also used h Print help message and quit v Print version number and quit Split the Glide job specified in the inp file into smaller subjobs for distributed execution The ligands between firstlig and lastlig inclusive are separated into njobs equal sized batches If omitted njobs defaults to 1 firstlig defaults to 1 and lastlig defaults to 0 which is interpreted to mean the final ligand in the ligands file Each use of para glide creates two scripts job report sh and job status sh The job report sh script collects the output poses from subjobs created by para glide and produces a single pose file and a single report file that summarizes the best poses in the entire job suite The job status script can be run while the job suite is running or afterward It summarizes the disposition of each job whether it finished normally died was terminated stopped and so on using the conventional Schr dinger job control terms See the Maestro User Manual for information about job monitoring and job control 110 FirstDiscovery 3 0 User Manual Chapter 6 Glide The j option is useful for preparing only a single subjob A value of 0 is equivalent to not specifying j at all and all subjobs will be printed Negative values are not permitted By default all jobs use the same input ligand file eac
145. gand Bonds If any covalent bonds exist between the protein and ligand they will preclude treatment in Glide or Liaison Bonds between the components of the protein metals cofactor structure were deleted in Section 4 7 3 4 9 Running ProteinPrep on the Structures From this point on all structural manipulations are done by the ProteinPrep panel shown in Figure 4 1 and its related scripts Before you open this panel ensure that the protein and ligand are in the Workspace To open the ProteinPrep panel select ProteinPrep from the Applications menu on the main menu bar ProteinPrep pprep Eeki Job ppreptmp Login saunders Host localhost 1 Note Make sure that your ligand cofactors and nonstandard residues have appropriate bond orders and formal charges before starting a job L B Pick ligand W Show markers I Procedure Preparation and refinement ww Preparation only vy Refinement only Neutralization zone around the ligand 4 10 20 A default x 8 12 A recommended for Liaison ww Do not neutralize residues Stop minimization when RMSD reaches 0 30 A Incorporate results as 4 Separate entries ww Single entry Start Write Job Files Hide Help Figure 4 1 The ProteinPrep panel FirstDiscovery 3 0 User Manual 51 Chapter 4 Protein Preparation 4 9 1 Entering Job Settings To enter job settings 1 Type a name for the job in the Job text box 2 Choose a host f
146. h job reading out of it just the ligands pertinent to that job If the s option is given a new ligand file is written for each subjob containing only the ligands for that subjob This is likely to be more efficient if there are a large number of ligands If the x option is given then the jobs are launched after the input files are written Any additional arguments you give on the command line are passed on to the impact command Therefore you can have the jobs run on a remote machine by specifying HOST hostname FirstDiscovery 3 0 User Manual 111 Chapter 6 Glide 112 FirstDiscovery 3 0 User Manual Chapter 7 Liaison 7 1 Brief Description of Liaison A Liaison simulation combines a molecular mechanics calculation with experimental data to build a model scoring function used to correlate or to predict ligand protein binding free energies A method of this type is called a Linear Response Method LRM a Linear Interaction Approximation LIA or a Linear Interaction Energy LIE method A novel feature of Liaison is that the simulation takes place in implicit continuum rather than explicit solvent hence the name Liaison for Linear Interaction Approximation in Implicit SOlvatioN The explicit solvent version of the methodology was first suggested by Aqvist Hansson T Aqvist J Protein Eng 1995 8 1137 1145 based on approxi mating the charging integral in the free energy perturbation formula with a mean value approach
147. hat is formulated to avoid overly rewarding charge charge interactions at the expense of charge dipole and dipole dipole interactions This score is intended to be more suitable for comparing the binding affinities of different ligands than is the raw Coulomb van der Waals interaction energy In the final data work up you can combine the computed GlideScore and modified Coulomb van der Waals score values to give a composite score that usually helps improve enrichment factors in database screening applications See the FirstDiscovery Technical Notes for more details This hierarchical search gives Glide exceptionally high accuracy in predicting the binding mode of the ligand At the same time the computational cost is dramatically reduced compared to what would be required for a complete systematic search The key to this reduction is that the algorithm allows the rotamer groups to be optimized one at a time for a given core conformation and location of the ligand For example if there are five rotamer groups and each has three rotamer states the total number of conformers in the ensemble based on this core conformation location is 3 243 However if the rotamer groups are optimized one at a time the number of conformational combinations is only 3x5 15 for a savings of about a factor of 15 in computational effort While many other time saving algorithms in Glide contribute to its performance advantages this fundamental qualitative f
148. he conjugate gradient minimization algorithm The default number of steps is 100 but you can choose any value greater than or equal to 0 A minimization of 0 steps does a single point current energy calculation on each pose that survives rough score screening or on the input pose if no screening was done If the Score each input structure in place option in the Ligand folder is selected the input pose is used 6 6 3 Final Scoring Section The controls in this section are related to the GlideScore method used in the final scoring of the poses The default is to reject a pose unless FirstDiscovery 3 0 User Manual 89 Chapter 6 Glide Coulomb vdW score lt If the pose has a Coulomb van der Waals score greater more positive than this value the pose is rejected The default value is 0 0 kcal mol This means that poses that interact favorably with the protein site however weakly are retained whereas poses that interact unfavorably are rejected For Glide 3 0 you should not change this value An exception might be for exploratory runs with actives that you know bind to the flexible receptor if you want to find out how well or poorly Glide s rigid receptor docking model treats them In such cases you might choose a large positive value such as 20 000 to make sure that you can track all of the known actives Hydrogen bond score lt In the current version of GlideScore each hydrogen bond with an appropriate H X
149. he Maestro menu To save a log file with a record of all operations performed in the current session click Quit save log file in the Quit panel This information can be useful to Schr dinger support staff when responding to any problem you report 26 FirstDiscovery 3 0 User Manual Chapter 3 FirstDiscovery from the Command Line 3 1 Command Line Capabilities This section outlines the capabilities of the FirstDiscovery suite as run from the command line rather than the Maestro GUI 3 1 Location of Files and Working Directory For both the FirstDiscovery and Basic Impact applications Maestro normally writes input files to the directory from which you launched Maestro called the Maestro working direc tory Impact also normally writes its output files to the same location though Impact input files and the Glide interface allow you to specify an arbitrary location for grid files The exception is Liaison where a directory hierarchy is created based on job names and on the names you assign to the individual ligands being simulated For more information see Figure 7 1 on page 115 and Section 7 4 on page 119 3 1 2 FirstDiscovery Job Types There are four types of FirstDiscovery jobs that can be run using the impact command Glide Liaison QSite and Basic Impact The procedure for starting Impact calculations from the command line varies depending on the job type Follow the specific guidelines listed in this chapter to ensure c
150. he QM region but only along with attached protein atoms The QM region must extend at least as far as the first permissible cut between protein atoms To select all atoms in a free molecule for inclusion in the QM region 1 Click Free ligands 2 Pick any atom in a free ligand to add all its atoms to the QM region This selection is used to add an entire ligand or other non covalently bound species to the QM region Free atoms such as metal ions are selected using the lons panel Ligands which are covalently bound to the protein cannot be added using this method because this method does not make any parametrized cuts To add covalently bound ligands to the QM region make either a pair of backbone cuts to select the residue to which the ligand is bound or make a side chain cut Basis set By default the basis set used for the entire QM region is 6 31G LACVP in the case of transition metals which is the basis set used in developing the parametrizations for the cuts If you wish to use a different basis set for any residue in the OM region select that residue in the QM region list then select another basis set from the Basis set menu Delete To remove a specific residue from the QM region highlight the residue in the QM region list and click Delete at the bottom of the panel When deleting individual residues take care to ensure that the resulting QM region is consistent with the QSite cuts previously made using the Residue sele
151. he supported sampling methods are Minimization Hybrid Monte Carlo This method employs the Hybrid Monte Carlo algorithm to sample the binding of the ligand to the receptor or the conformation of the free ligand See Chapter 11 for details on the Hybrid Monte Carlo task and settings When simulation as opposed to minimization is used for sampling HMC is the rec ommended option Molecular Dynamics This method employs a Molecular Dynamics algorithm to sam ple the binding of the ligand to the receptor or the conformation of the free ligand See Chapter 10 for details on the Dynamics task and settings Minimization algorithm This menu is available for all three sampling methods there is an option to Minimize before simulation for the HMC and MD sampling methods You may choose the Truncated Newton Conjugate gradient or Steepest descent method to locally minimize the ligand receptor or free ligand geometry See Chapter 9 for details on the Minimization task and settings FirstDiscovery 3 0 User Manual 125 Chapter 7 Liaison Liaison Job fit sim Login saunders Host localhost 1 settings System Parameters Constraints Snalysis Sampling method Minimization Minimization algorithm Truncated Newton Shnulation temperate KY 300 Temperature relaxation Une ips 0 01 Residue based cutoff distance 15 00 A Force field OPLS A amp _ Use ligand input partial charges if they exis
152. hen include or exclude them from the Entry menu Inclusion with the mouse works just like selection when you include an entry by clicking all other entries are excluded It is sometimes useful to keep one entry in the Workspace and include others one by one for example a receptor and a set of ligands You can fix entries in the Workspace by selecting the entries and choosing Fix from the Entry menu or by pressing ALT F A padlock icon replaces the diamond in the In column to denote a fixed entry To remove a fixed entry from the Workspace you must exclude it explicitly ALT X It is not affected by the inclusion or exclusion of other entries Fixing affects only the inclusion of the entry you can still rotate translate or modify the structure 2 4 5 Mouse Functions in the Project Table The Project Table supports the standard use of shift click and control click to select objects This behavior applies to the selection of entries and the inclusion of entries in the Workspace Dragging to resize rows and columns and to move rows is also supported You can drag a set of non contiguous entries to reposition them in the Project Table When you release the mouse button the entries are placed after the first unselected entry that precedes the entry on which the cursor is resting For example if you select entries 2 4 and 6 and release the mouse button on entry 3 these three entries are placed after entry 1 because entry 1 is the first unsele
153. hey are distant from the active site Struc tures that are missing residues near the active site should be repaired Check the protein structure for metal ions and cofactors e Set charges and correct atom types for any metal atoms as needed Set bond orders and formal charges for any cofactors as needed 5 Adjust the ligand bond orders and formal charges 6 Run protein preparation Open the ProteinPrep panel mark the ligand choose the desired Procedure and click Start 7 Review the prepared structures If problems arise during the preparation or refinement stages review the log file correct the problems and rerun Examine the refined ligand protein water structure for correct formal charges 38 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation and protonation states resulting from Step 6 and make final adjustments as needed 4 4 Importing the Protein Complex Structure This step begins the protein preparation procedure For an introduction to the Maestro interface see Chapter 2 For help with the ProteinPrep panel or any Maestro command or procedure see the online help or the Maestro User Manual To reverse your most recent Maestro action you can click the Undo button on the toolbar i To import a ligand receptor protein complex structure into Maestro On the toolbar click the Import structures button E The Import panel is displayed Select PDB format Enter the name o
154. hoose Glide function Set up grids a choase docking mode Displayed structure is Receptor alone A Skip uands with 80 atoms Skip ugands with 15 ratatable homis Base name for grid files grids H01 EI Directory for grid files home saunders Documentation FirstDiscov Start Write Job Files Hide Help Figure 6 3 The Settings folder of the Glide panel FirstDiscovery 3 0 User Manual 71 Chapter 6 Glide Using Extra Precision XP Mode Extra precision mode should be run only on ligand poses that have scored well in a Glide standard precision run Do not use XP mode in systems where the active site contains a metal atom To use XP mode 1 Set up a Glide docking job choosing docking mode Standard speed and precision to run on the entire ligand set 2 In the Output folder of the Glide panel under Structure output Select Write ligand pose file filename lib mae exclude receptor Make sure that the default value 1 is specified in the number field of Keep at most n poses per ligand 3 When the standard precision job is complete determine which poses are high scor ing enough to be run again using XP mode A rule of thumb is to include the highest ranking 2046 of the poses as docked by SP Glide i e 200 poses for each 1000 database ligands In some cases the top 10 may suffice while in others 3096 may be required Such judgements can be made however only if you
155. hoose Selected entry instead of Workspace as the Source of job input your frozen atom set is not used 9 5 3 The Buffered Atoms Panel Use the Buffered Atoms panel to specify a set of atoms to be harmonically restrained during an Impact minimization calculation or dynamics simulation Such atoms are referred to as buffered atoms because they are often used as a buffer between totally free and totally frozen regions The Buffered Atoms panel is opened by clicking the Buff ered Atoms button in the Constraints folder The upper portion of the Buffered Atoms panel displays the list of atom numbers that are to be buffered restrained with a harmonic potential Below this list is the Buffer Force text box which sets the force constant to be applied to the buffered atoms The default buffer force setting is 25 00 kcal A mol To define buffered atoms use the Pick options the All button or the Atom Selection dialog box click the blue Select button Selected atoms are listed at the top of the Buffered Atoms panel If Show Markers is selected the atoms to be buffered are marked with a blue cross and a spring icon in the Workspace These markers can be hidden by deselecting Show Markers in the ASD The Delete button at the bottom of the panel removes the currently selected buffered atom from the list The Delete All button removes all currently defined buffered atoms from the list Note These buffered atom selections are keyed
156. ich runs the quantum mechanical part The Jaguar component can be run in parallel if multiple processors are available either from the command line or from the GUI The command line switches optional and required for running QSite calculations are described in Table 3 4 The syntax for specifying the two input files is SSCHRODINGER impact j jag jobname in i jobname inp It is important that jag jobname differ from jobname so that working files and directories for the two programs do not collide so Maestro does this automatically For a QSite job set up from a session in which you enter the job name jobname Maestro names the Impact input file jobname inp and the Jaguar input file jobname jaguar in FirstDiscovery 3 0 User Manual 33 Chapter 3 FirstDiscovery from the Command Line Table 3 4 QSite Command Line Options Syntax Example Description j jag_jobname in Required specifies the Jaguar input file jag jobname in p num Specifies the number of processors to use for Jaguar i jobname inp Required specifies the Impact input file jobname inp o logfile Specifies the file name for standard output and standard error If omitted jobname 1og is used 3 4 5 Basic Impact Basic Impact calculations can be started at the command prompt using the syntax shown below S SCHRODINGER impact i jobname inp o logfile Basic Impact jobs require only the i option to specify the input file If you want the log
157. igand bounding box is 10 on a side The ligand center used to position the ligand at a site point is different from the Ligand centroid that serves as one choice for positioning the enclosing box and bounding box For example in rigid docking runs the ligand center is taken as the midpoint of a line drawn between the two most widely separated ligand atoms Example cases suggest that the ligand center and the ligand centroid computed as the average of the smallest and largest x y and z coordinates of any atom typically differ by 1 2 A For flexible docking the difference can easily be greater for here the ligand center is defined for each core confor mation generated by Glide as the midpoint of the line between the two mostly widely separated atoms in the core To ensure that the bounding box is not unrealistically small Maestro sets a minimum value of 10 Note that the position of the centroid of a set of selected active site residues can vary even more widely from the ligand center This is something to keep in mind when selected active site residues are used to set the box centers Size of enclosing box As previously noted the enclosing box is the box that must contain all ligand atoms during the docking procedure There are two ways to determine the size of this box but the maximum size is 50 on a side 76 FirstDiscovery 3 0 User Manual Chapter 6 Glide The Fit displayed ligand option is available if a recept
158. ihedral measurement and to delete Workspace inter or to delete H bonds measurements 2 3 3 Mouse Functions in the Workspace The middle and right mouse buttons have special uses in the Workspace These can be used on their own and in combination with the SHIFT and CTRL keys to perform common operations such as rotation translation centering and zooming Apart from centering a molecule on an atom all these operations involve dragging Table 2 1 Mapping of Workspace operations to mouse actions Operation Action Rotate about the x and y axes Drag with middle mouse button Rotate about the x axis only Drag vertically with SHIFT and middle mouse button Rotate about the y axis only Drag horizontally with SHIFT and middle mouse button Rotate about the z axis Drag horizontally with CTRL and middle mouse button Spot center on an atom Right click Translate in the x y plane Drag with right mouse button Translate along the y axis Drag vertically with SHIFT and right mouse button Translate along the x axis Drag horizontally with SHIFT and right mouse button Translate about the z axis Drag horizontally with CTRL and right mouse button Zoom Drag horizontally with middle and right mouse buttons or with SHIFT CTRL and middle mouse button 2 3 4 Shortcut Key Combinations Some frequently used operations that can be performed in the main window have been assigned shortcut key combinations The shortcuts their functions and their me
159. in contains both metal ions and cofactors do all procedures check metal ion properties as described in Section 4 7 3 check cofactor properties as described in Sections 4 7 4 and 4 7 5 then proceed to Section 4 8 4 7 3 Adjusting Metal Ions Metal ions in the protein complex cannot have covalent bonds to protein atoms Prepara tion jobs run from the ProteinPrep panel now automatically delete protein metal bonds Therefore there is usually no need to explicitly delete the bonds before checking and adjusting element names and formal charges FirstDiscovery 3 0 User Manual 45 Chapter 4 Protein Preparation To manually delete bonds between metals and protein atoms where necessary 1 On the toolbar click hold the Delete button selecting Bonds from the button menu 2 Click on the bonds to be deleted The MacroModel atom types for metal ions are sometimes incorrectly translated into dummy atom types Du Z0 or 00 when metal protein bonds are specified in the input structure Furthermore isolated metal ions may erroneously be assigned general atom types GA GB GC etc The ProteinPrep procedure cannot treat structure files containing these atom types they should be corrected as described in this section To display element labels and formal charges 1 Open the Build panel by clicking the Show Hide build panel button 2 In the Build toolbar click the Label button Fh All metal ions and other heteroatoms are labeled with
160. in which the integral is represented as half the sum of the values at the endpoints namely the free and bound states of the ligand The empirical relationship used by Liaison is shown below AG a XU 4 lt U aw gt B US gt lt U tec Y XU9 gt Ul uo Here lt gt represents the ensemble average b represents the bound form of the ligand f represents the free form of the ligand and a B and y are the coefficients U gw Uciees and U are the van der Waals electrostatic and cavity energy terms in the Surface General ized Born SGB continuum solvent model The cavity energy term U a is proportional cav to the exposed surface area of the ligand Thus the difference gt lt Uf_ gt cav cav lt U measures the surface area lost by contact with the receptor The net electrostatic interac tion energy in continuum solvent is given by U elec U cou y 2 U renf where Usoni is the Coulomb interaction energy and U is the SGB solvent reaction field energy The factor of 2 compensates for the division by 2 made in the definition of the reaction field free energy In most applications the coefficients a B and y are determined empirically by fitting to the experimentally determined free energies of binding for a training set of ligands In such applications Liaison s Simulate task is used to calculate the values of U 4w U etec and U sa for the bound complexed and unbound free sta
161. ination of duplicate poses clustering Discard pose as duplicate if RMS distance 0 5 and maximum atomic displacement 1 3 A Structure output Write pose viewer file dock_confgen_py mae include receptor Q Write ligand pose file dock_confgen_lib mae exclude receptor Keep at most 1000 poses Keep at most 1 poses per ligand Start Write Job Files Figure 6 10 The Output folder of the Glide panel from a pose previously selected for inclusion in the reported output You can choose any values greater than 0 0 A The rms distance is based on a comparison of heavy atom non hydrogen coordinates 6 7 7 Structure Output Section The options in this section are described below FirstDiscovery 3 0 User Manual 91 Chapter 6 Glide Structure output The final list of poses that pass Glide s criteria is written to a multi structure Maestro file The options are Write pose viewer file jobname_pv mae This option includes the receptor structure in the output Maestro file job name pv mae where jobname is taken from the Job text box in the upper left of the panel This version of the Pose File is intended for use with Maestro s Glide Pose Viewer facility Write ligand pose file jobname_lib mae This option causes only ligand structures to be written to the output Maestro file jobname lib mae where jobname is taken from the Job text box found at the upper left of the panel This file also
162. inations o dece intere Renee etse eia pare ERRARE 11 24 Maestro PRO CCIB oec re eter oett e rente EDI Ep HE eT PU 12 2 4 1 The Project Table Toolbar tritt rre niet trenes 13 241 2 The Project Table MenUus edet te Peers 15 2 4 5 Selecting ENIES euer eret t rre ever Pere eie HER tesa ee ERR ee 15 2 4 4 Including Entries in the Workspace eere 16 2 4 5 Mouse Functions in the Project Table eese 16 2 4 6 Project Table Shortcut Keys erede rte etre emer eer Enn 17 2 5 Building a SUBIT ose nta eR e eere eter eces e Re be Rye Ue A EEES 18 2 6 Selecting Atoms ece ditione n mh eee rH URP PEE ETAS 21 2 7 Maestro Command SoOFIpls ied ere EPOR s e SERE E EE oaeiae 22 2 8 Specifying a Maestro Working Directory eese 23 2 0 Undoing an Operation ose ere terere tee Eaa esI PNE eB e ers 24 2 10 Running and Monitoring Jobs esee 24 ATE Getin Helps err EHE REUS ca Risa E EN 26 2 12 Endine d Maestro SessiOis cria e ibvs Deeper uev oue VIE EE eae 26 Chapter 3 FirstDiscovery from the Command Line eese 27 3 1 Cominand Lane Capabilities eL tee teri ke e a 27 3 1 1 Location of Files and Working Directory sese 27 3 12 Fargubuscovery JOD Ty Mesias srt tesi rosnie i a is ERE 27 FirstDiscovery 3 0 User Manual iii Contents 3 1 3 Reasons to Run Jobs from the Command Line
163. ing existing entries Do not incorporate Potential Constraints MD Parameters HybridMc Number of HMC cycles 100 MD steps per HMC cycle 4 Time step ps 0 001 Target temperature K 298 15 Start Write Job Files Hide Help Figure 11 1 The HybridMC folder of the Impact Hybrid Monte Carlo panel 174 FirstDiscovery 3 0 User Manual Chapter 11 Hybrid Monte Carlo Simulations Time step This text box sets the MD global time step in picoseconds for the simulation The default value is 0 001 ps The acceptable range is any value greater than 0 ps Because energy conservation is less important in HMC simulations a time step of 0 002 ps or greater may be suitable Target temperature This text box sets the target temperature in Kelvin for the HMC simulation The default initial temperature is 298 15 K The default target temperature is also 298 15 K The acceptable range is any value greater than 0 K FirstDiscovery 3 0 User Manual 175 Chapter 11 Hybrid Monte Carlo Simulations 176 FirstDiscovery 3 0 User Manual Chapter 12 Soak Add Explicit Water Solvent 12 1 Using the Soak Panel Soak surrounds the molecule or molecules currently in the Workspace with a box of solvent molecules You specify the box size and the requested solvent density Then Impact adds the solvent molecules removes any that are too close to the solute and writes out a Maestro format file jobname out mae for
164. is 0 25 Scale by Van der Waals radii of nonpolar receptor atoms are multiplied by this value The default is not to scale receptor atom radii and therefore this value is set to 1 00 For ordinary Glide docking it is recommended that receptor radii be left unchanged and any scaling be carried out on ligand atoms as described in Section 6 5 on page 80 Display bounding box for ligand center green Select this option to display the ligand center bounding box deselect it to undisplay the box The bounding box is drawn as a green wireframe cube in the Workspace The center of the cube is marked in green by the x y and z axes Display enclosing box purple Select this option to display the enclosing box deselect it to undisplay the box The enclosing box is drawn as a purple wireframe cube in the Workspace FirstDiscovery 3 0 User Manual 77 Chapter 6 Glide 6 4 2 The Ligand to Define Grid Panel The Ligand to Define Grid panel is used to select the ligand Maestro uses to center the Glide enclosing box and bounding box To open the panel select Ligand centroid in the Site folder and click Specify Ligand The selection options of the Ligand to Define Grid panel are described below Use displayed ligand This button requires that the Workspace structure contain a ligand molecule and that the ligand already be identified e g via the Choose an atom in the ligand molecule button on the Settings folder The displayed ligan
165. ison Dynamics and HMC jobs Ligand Directory or Directories The directory or directories created under the Master Liaison Run Directory The names of the directories are defined by ligand names that you specify FirstDiscovery 3 0 User Manual 115 Chapter 7 Liaison 7 3 3 Files Created In the Maestro working directory the following files are created change_sgbparam_jobname Utility to modify the SGB solvation parameters for the input files in all the ligand subdirectories simulate_jobname The main script Maestro uses to dispatch the Liaison simula tion jobname mae The receptor or receptor ligand structure file in Maestro format This file is written by the Maestro interface analyze jobname Script to run a Liaison analysis fitting or predicting job jobname in Input file for a Liaison analysis job jobname dat Data file for a Liaison analysis job jobname log Log file for a Liaison analysis job jobname out Output from a Liaison analysis job In the Master Liaison Run Directory the following files are created jobname 10g Log of ligands submitted For each ligand in the job two files are created but these are generally of interest only if an error has occurred ligand 1log ligand stdout In the Ligand directory or directories the following files are created 116 jobname free inp The Liaison input file for simulation of the free ligand jobname bound inp The Liais
166. ite Ligand Scoring output Constraints simitarity In order to apply docking constraints select the receptor sites in the list below Display Receptor Receptor constraint sites W Show markers Ligand atoms interacting with receptor metal sites Must be charged a Start Write Job Files Hide Help Figure 6 11 The Constraints folder of the Glide panel 96 FirstDiscovery 3 0 User Manual Chapter 6 Glide 6 8 3 Glide Constraints Folder Features Docking Once you define Glide constraints in grid generation you can apply these constraints to docking jobs During setup of the docking job return to the Constraints folder and select up to four sites from the list The same set of grids can be used for docking jobs with or without constraints The following features appear in the Constraints folder when Dock one or more ligands has been selected in the Settings folder Display Receptor Click this button to display the receptor in the Workspace If Show markers has not been deselected every receptor constraint site defined in grid generation will be marked Show markers Selected by default this option marks possible receptor constraint sites with red crosses and padlocks You must still select a constraint from the list to employ it during docking Receptor constraint sites The Glide constraints defined in the receptor grids are listed in this box Each atom is identified by atom number atom type residue t
167. ite folders Potential Constraints and Minimization share most of their features with the Potential Constraints and Minimization folders in Basic Impact applica tion panels such as Impact Energy Minimization These shared features are described in Chapter 9 Energy Minimization The QSite panel Potential folder contains settings for the MM potential energy function one of which continuum solvation affects the QM potential energy as well Note The following methods and options are not available for QSite calculations Fast Multipole Method FMM periodic boundary conditions and Ewald summation and treatment of continuum solvation using the Surface Generalized Bohr SGB method The molecular mechanics force field used in QSite is the OPLS1999 version of OPLS AA QSite Potential Folder Options See Section 9 4 1 for a description of the options for Electrostatic treatment and Dielectric constant 140 FirstDiscovery 3 0 User Manual Chapter 8 QSite QSite qsite Job gsitetmp Login dyal Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries lt gt Replacing existing entries lt gt Do not incorporate Potential Constraints Minimization Optimization QM Settings Electrostatic treatment Constant dielectric Dielectric constant 1 0 J Use non bonded cutoffs Use continuum solvation Start Write Job Fil
168. ith a value Sans serif ALT H Keyboard keys uppercase In descriptions of command syntax the usual UNIX conventions are used square brackets enclose optional items braces enclose required items and the pipe symbol separates items in a list from which one item must be chosen In this document to type a command means to type the required text in the specified loca tion and to enter a command means to type the required text then press the RETURN key 1 2 Introduction to FirstDiscovery Panels FirstDiscovery panels in Maestro have a common structure with standard features and options in the upper and lower regions of the panel 1 2 1 Job Options At the top of the panel are job options The first three features are common to FirstDis covery Protein Preparation Glide Liaison and QSite as well as Impact panels Job The default file name for jobs started from a panel is displayed in the Job text box e g glidetmp or impacttmp It is recommended that you change the default to a different job name for each new job When a job is started several files are created using the job name as the base name for the file names If the new job has the same name as the previous job Maestro does not automatically assign new names to jobs or files it overwrites the files with data from the new job Files from the first job will not be recoverable 2 FirstDiscovery 3 0 User Manual Chapter 1 Introduction Login To run Impact on
169. ject by For a description of these options see Section 1 2 The default job name for Impact Energy Minimization jobs is impacttmp The input structure for an Impact Energy Minimization job can be either the contents of the Workspace or a single entry in the Project Table To perform energy minimization on a system composed of multiple entries 1 Include only those entries in the Workspace 2 Select Workspace as the Source of job input FirstDiscovery 3 0 User Manual 153 Chapter 9 Energy Minimization 9 3 Energy Minimization Panel Features The Energy Minimization panel has three tabbed folders Potential Constraints Minimization All three folders are described in detail in this chapter The QSite panel includes versions of these three folders The first two folders also appear in the Maestro panels of two other Basic Impact applications Molecular Dynamics Simulations and Hybrid MC Simulations 9 4 The Potential Folder The Potential folder sets parameters that control how Impact calculates the molecular mechanics energy in a minimization calculation or dynamics simulation The panels for three Basic Impact Applications and for QSite each include a Potential folder Open the the folder by clicking the Potential tab which is always the first tab from the left 9 4 1 Potential Folder Options The options in the upper portion of the Potential folder are described below Force field This option menu sets the molecul
170. l charge default 2 mg maxgroups count Maximum number of ion groups to handle default 15 mo maxoutcts count Maximum number of output structures per input struc ture default 512 sm showmatches Show substructure pattern matches sf showfinal Show final ionization candidate list 11 loglevel level Expansion report log level ss showskips kp keep_props strict Use 0 for quietest default Use 1 to log state generations Use 2 to log ion fragment fusions too Show skipped state generations Augments log level 1 and up Log levels gt 1 give skip reasons Retain all properties in output CTs Absent this option connectivity dependent properties are cleared Terminate run if any input CT is bad Unsets default fault tolerant mode Bad structure file option is ignored s spec specfile specfile Use nonstandard patterns spec file rw retitle_with prefix Add ion state number onto structure titles For a more detailed usage summary use the command For comple 64 SSCHRODINGEI SSCHROI DINGE R utilities ionizer doc te documentation on the ionizer see the README file R services vversion doc README ionizer FirstDiscovery 3 0 User Manual Chapter 6 Glide This chapter contains A brief introduction to the Glide Grid based Ligand Docking with Energetics pro gram its scientific methods and computational procedures A detailed description of the Glide pa
171. l click the entry or the In column 2 4 6 Project Table Shortcut Keys Some frequently used project operations have been assigned shortcut key combinations The shortcuts their functions and their menu equivalents are listed in Table 2 4 Table 2 4 Shortcut keys in the Project Table Keys Action Equivalent Menu Choices ALT A Select all entries Select gt All ALT F Fix entry in Workspace Entry gt Fix ALT I Show import panel Table gt Import Structures ALT N Include only selected entries Entry gt Include Only ALT U Deselect all entries Select gt None ALT X Exclude selected entries Entry gt Exclude ALT Z Undo Redo last command Edit gt Undo Redo in main window FirstDiscovery 3 0 User Manual 17 Chapter 2 Introduction to Maestro 2 5 Building a Structure After you start Maestro the first task is usually to create or import a structure You can open existing Maestro projects or import structures from other sources to obtain a struc ture To build a structure you use the Build panel which you can open by choosing Frag ments from the Edit menu or by clicking the Show Hide Build panel button in the toolbar The Build panel allows you to create structures by drawing or placing atoms or fragments in the Workspace and connecting them into a larger structure to adjust atom positions and bond orders and to change atom properties This panel contains a toolbar and three folders The Fragments folder offers a v
172. layed ligand Dock ligand s from files When this button is on one or more ligands will be read from one or more structure files and docked by Glide instead of or in addition to the currently displayed ligand Using multiple files is supported only for PDB format and each PDB file must describe one ligand Maestro and SD file formats allow multiple structures to be included in one file but only one Maestro or SD file can be specified here 80 FirstDiscovery 3 0 User Manual Chapter 6 Glide Glide glide Job dock_confgen Login saunders Host localhost 1 settings site Ligand Scoring output Constraints simitarity xv Dock selected entries from project table Dock ligand s from files Ligand structure file format Maestro Specify one file in Maestro format Add File Dock all structures from ligand file xv Dock range of structures from file 1 Te 1000 Docking scoring mode Generate conformations for each input structure flexible docking Q Dock each input structure rigidly ww Score each input structure in place scoring output file dock confgen scor W Allow amide bond rotations WW Allow ring flips Scaling of vdW radii for nonpolar ligand atoms Scale radius if partial atomic charge lt 0 15 Scale by 0 80 _ Define a reference ligand Start Write Job Files Hide Help Figure 6 7 The Ligand folder of the Glide panel Ligand struct
173. le for writing output and log messages If the o option is omitted Impact will name the log file jobname 1og where jobname is taken from the Impact input file name Use specific size version of the Impact executable Acceptable values for the s parameter are medium or huge If omitted medium is assumed in most cases it is valid for up to 8000 atoms or 8000 bonds Run a Liaison simulation job using ligand directory dir If the d switch is omitted dir must be the last argument on the command line Specifies name of control file for fit predict jobs Specifies name of data file for fit predict jobs Specifies optional name to use for fit predict jobs Specifies optional output file name for fit predict jobs Specifies the Jaguar input file Specifies the number of processors to use with Jaguar Table 3 3 Schr dinger Job Control Options Option HOST host HOST host n HOST hostl host2 USER user 30 Description Specify a remote machine optionally its number of processors n on which to run an Impact job Can also be used to specify a batch queue to submit the job to or a collection of hosts for distributed or parallel jobs Default is to run on the local host See Section 3 4 Specify a remote user name to run Impact job under Default is to use the local user name FirstDiscovery 3 0 User Manual Chapter 3 FirstDiscovery from the Command Line Table 3 3 Schr dinger Job Control Options Continued
174. llel processing 148 job control commands 34 JODn rie tr geh p Eaa 169 jobs running senusien 31 34 jobs running in Maestro 24 25 K keywords Jaguar seen 148 killing Liaison jobs ses 137 K space vectors maximum length 159 L levels number of in FMM 158 Liaison Analysis reti ten SERERE 118 Analysis folder 132 Constraints folder 130 deseribed ieieee tree te 113 directory structure 27 LIS distributed processing 123 136 fitting simulation results 118 Impact atom constraints 160 job files created wt 116 killing jobs ies 137 methodology eee 113 multiple processors 121 136 184 panel in Maestro sess 119 Parameters folder 125 predicting binding affinities 119 running from the shell 136 running remotely essss 114 running through Maestro 114 Settings folder sss 120 System folder tere 122 Liaison Impact constraints 130 license LigPiep ceciren ieiti 60 ligand receptor interaction Glide
175. ltiplicity text boxes can be edited manually If the value in the Charge text box does not match the sum of the formal charges of the atoms in the QM region Maestro displays a warning message but allows you to proceed If there is a discrepancy between the total charge and the multi plicity Jaguar will halt with an error message The charge and multiplicity of the QM region must be mutually consistent FirstDiscovery 3 0 User Manual 147 Chapter 8 QSite QSite qsite lei Job gsitetmp Login dyal Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries Replacing existing entries lt gt Do not incorporate Potential Constraints Minimization Optimization QM Settings Method DFT B3LYP Charge 0 Multiplicity 1 QM options iacc 1 vshift 1 0 maxit 100 Number of processors to run job 1 QM regions Residues Ligands lons Start Write Job Files Hide Help Figure 8 5 The QM Settings folder of the QSite panel QM options This text box can contain any Jaguar keywords such as print flag settings non default convergence criteria and so on Each such option is of the form keyword value with no embedded blanks Multiple keyword value pairs can be specified separated by one or more blank spaces By default the following QM options appear in the box iacc 1 vshift 1 0 maxit 100 You can rem
176. maximum displacement allowed for an atom in any step of a minimization calculation Convergence criteria This option menu sets the convergence criteria for the minimization Either or both of two criteria energy change and gradient can be specified Thus the options are Energy and Gradient Choosing this option allows access to both the Energy change criteria and Gradient criteria text boxes Energy change criteria Use this text box to specify the value of the energy change criterion The default value is 107 kcal mol but any positive value is allowed The criterion is satisfied if two successive energies differ by less than the specified value Gradient criteria Use this text box to specify the value of the gradient criterion The default value is 0 01 kcal mol but any positive value is allowed The criterion is satisfied if the norms of two successive gradients differ by less than the specified value Long Range Forces Options for Truncated Newton minimizations Update long range forces every n steps This option is available only for the Trun cated Newton algorithm The default is to update long range forces every 10 steps Between updates estimates of these forces are used Smaller values of n more fre quent updates can be used to improve convergence but will make the optimization slower The maximum recommended value is 20 Long range force cutoff gt n Angstroms This option is available only for the
177. me to increase or decrease during pressure fluctuations in the system The default is the value for water 4 96 x 10 atm The acceptable range is any value greater than zero Effective density This text box specifies the effective density g cm of the solute molecules This quantity is used to compute long range corrections to the pressure during NPT molecular dynamics simulations The default value is 1 0 g cm The acceptable range is any value greater than zero Volume scaling Select one of two options for volume scaling in a MD simula tion Molecule center of mass default This method of volume scaling is best for small molecules and is implemented by scaling the coordinates of the center of mass for each molecular species relative to the center of the simulation box Atom based This method of volume scaling is best for large molecules and is implemented by uniformly scaling all atomic coordinates relative to the center of the simulation box Initialize velocities from gaussian distribution Selecting this option initializes the velocities of the molecules from a Gaussian distribu tion The Initial temperature text box becomes available when this button is selected Initial temperature This text box is available for all three ensembles when Initialize velocities from gaussian distribution is selected It sets the initial temperature for the MD simulation The default value is 298 15 K The acceptable range is any value great
178. ms in the scoring function that reward hydrophobic contact between the protein and the ligand appropriate hydrogen bonding interactions etc The chief advantages of the XP method are to weed out false positives and to provide a better correlation between good poses and good scores Extra precision mode is a refinement tool designed for use only on good ligand poses The more extensive XP docking method and specialized XP scoring method are strongly coupled the more precise poses produced by XP docking are necessary for the more demanding XP scoring method Because XP docking mode requires more CPU time you should screen large sets of ligands first in standard precision mode Only the top scorers should be docked using XP mode Note If the active site of the complex contains a metal XP mode should not be used For information on using XP mode see Section 6 3 on page 70 See the FirstDiscovery Technical Notes for details about extra precision mode and for a discussion of results 6 1 3 Glide Prime Induced Fit Glide docking uses the assumption of a rigid receptor Scaling of van der Waals radii of nonpolar atoms which decreases penalties for close contacts can be used to model a slight give in the receptor and or ligand This may not be sufficient to treat systems where ligand binding induces substantial conformation changes in the receptor induced fit Schrodinger has developed a procedure for such cases which uses Prime and Gli
179. n If desired change the default value of 100 for Maximum number of iterations before proceeding to the QM Settings folder By default both the MM region and the QM region will be optimized If you want to optimize only the QM region simply set the number of FirstDiscovery 3 0 User Manual 145 Chapter 8 QSite minimization steps to 0 in the Minimization folder There is no need to explicitly freeze all of the MM atoms Maximum number of iterations This box controls the number of optimization iterations for minimization and transition state calculations The default is 100 iterations TS method If you select Transition state from the Method menu the default option for TS method is Standard The following three methods for transition state optimization are supported in QSite corresponding to well known ab initio techniques See the Jaguar User Manual for detailed information about these methods e Standard The standard transition state optimization method is useful if you have only a single initial guess structure the structure in the Workspace for the transi tion state It attempts to find the saddle point closest to the starting structure by max imizing the energy along the lowest frequency mode of the Hessian and minimizing the energy along all other modes LST Linear Synchronous Transit is useful if you have initial guess structures for the reactant and the product and want QSite to look for a transition state structure by
180. n how they compare to specified sets of active or inactive molecules Including similarity scoring in Glide docking jobs can yield significantly improved enrichment factors in database screening experiments Glide determines the similarity of two molecules by comparing lists of their atom pairs AP An atom pair is defined by two atoms and the number of bonds in the shortest path connecting them For similarity scoring purposes each atom is characterized by an atom type that depends on its atomic number neighbors bond orders and formal charges These atom types are different from those associated with force fields used elsewhere in FirstDiscovery Two molecules with no APs in common are assigned a similarity score of 0 0 and two with identical AP lists have a similarity of 1 0 Using similarity scoring in a Glide docking job entails adjusting the GlideScore of each ligand by a function based on a similarity score Glide can use either of two methods for calculating this similarity score Standard Similarity Scoring and Weighted Similarity Scoring In Standard Similarity Scoring each ligand is compared to a set of known actives All atom pairs that a given ligand has in common with a given active compound are counted equally and the similarity score for a ligand with respect to an active compound depends only on the number of such matches normalized by the total number of atom pairs in the two molecules For Standard Similarity Scoring
181. n one entry is selected in the project an error message will appear This option is incompatible with selecting Frozen or Buffered Atoms constraints Incorporate output into project by When a QSite or Basic Impact job is completed the structural results are incorporated into the project that was open when the job was started The choice of option determines how this is done Appending new entries default Each structure in the output file is added to the project as a new entry Replacing existing entries Any entries that served as input for the job are replaced with the new structures returned from the calculation Do not incorporate No change is made to the project when the job is complete FirstDiscovery 3 0 User Manual 3 Chapter 1 Introduction 1 2 2 Panel Controls and Tabbed Folders Controls that are specific to a panel appear in the middle section of the panel Usually the controls will be contained in a series of tabbed folders Each folder contains settings rele vant to the task that the panel performs 1 2 3 Start Write Hide and Help All FirstDiscovery panels have the following buttons in the lower portion of the panel Start Submits the job to the specified Host Write Job Files Writes out files required for the job without starting the job The job can be run from the command line in a UNIX shell Hide Dismisses the current panel without starting the job or writing any files Unlike other pan
182. n the ASD For more information about the Frozen Atoms panel see the Maestro online help as well as Section 9 5 2 on page 161 Note These frozen atom selections are keyed to the Workspace structure that you see on screen Jobs will only include these constraints if they are run on the Workspace structure Buffered Atoms Clicking this button opens the Buffered Atoms panel which selects atoms to be treated as buffered Buffered atoms are allowed to move subject to harmonic penalty function restraints that tether them to their initial positions The Buffered Atoms panel includes atom selection options like those in the Frozen Atoms panel and a Buffer Force text box for setting the force constant applied to the buffered atoms The default buffer force setting is 25 00 kcal mol A strategy for allowing receptor atoms closest to the ligand to move freely while restraining buffering a range of atoms at intermediate distance from the ligand and fixing freezing still more distant atoms would be to use ASL first to define as buffered all atoms more than 8 from the ligand and then to define as frozen all atoms more than 12 from any atom of the ligand If the ligand was loaded first into the Workspace and therefore is molecule 1 the Maestro commands needed to carry out this partitioning would be impactbufferedset beyond 8 mol n 1 impactfrozenset beyond 12 mol n 1 Because only the last state assigned to an atom is retain
183. nabled only for Predict jobs It allows the ligands to be specified via a user created text file the Read Ligand Names from a Text File option or by entering a comma separated list of names the Enter List of Ligand Names option 134 FirstDiscovery 3 0 User Manual Chapter 7 Liaison File Name This entry specifies a user created text file that contains the names of the ligands whose binding energies will be predicted The names can appear in the file as a comma sepa rated space separated or carriage return separated list For example 1bkm 3m 1 1bkm 3m 2 1bkm_3m_3 These entries instruct Maestro to retrieve the requisite data from completed Liaison simu lations from directories 1bkm 3m 1 1bkm 3m 2 and 1bkm 3m 3 under the Master Liaison Run Directory as defined by the jobname entered in the Job text box and is positioned under the Maestro working directory Thus one such directory path would be home user liaison 1bkm 3m 1 if home user is the Maestro working directory and 1iaison is the Master Liaison Run Directory For a small number of ligands it may be more convenient to use the Comma separated List option Comma separated List One or more ligands can be specified by entering a comma separated list of ligand names into the text box For example 1bkm 3m 1 1bkm 3m 2 lbkm 3m 3 Each of these names must correspond to a directory under the Master Liaison Run Direc tory See the preceding discussion under File Nam
184. name from the command line For usage summary information use the h help option SSCHRODINGER protprep h SSCHRODINGER utilities utilityname h FirstDiscovery 3 0 User Manual 35 Chapter 3 FirstDiscovery from the Command Line 36 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation 4 1 Protein and Ligand Structure Preparation Because the quality of results depends on reasonable starting structures Schr dinger offers a comprehensive protein preparation facility designed to ensure chemical correct ness and to optimize protein structures for use with FirstDiscovery It is strongly recom mended that you process protein structures with the preparation facility in order to achieve best results This chapter describes the preparation of protein ligand complexes using the FirstDis covery protein preparation facility Most features of the facility are available from the ProteinPrep panel Additional features are available in the command line application protprep The utilities pprep and impref are also available Use of the command line application and utilities is summarized in Section 4 11 on page 55 4 20 The ProteinPrep Panel The ProteinPrep panel is intended to help in preparing protein structures from PDB files for use in the FirstDiscovery applications Glide Liaison and QSite A typical structure downloaded from the Research Collaboratory for Structural Bioinformatics RCSB website http www r
185. nd Impact for the MM calculations Ligands and other specified regions of a protein complex can be studied using QM while MM is used for the rest of the molecule At each step of a QM geometry optimization Impact calculates energy terms for MM QM region interactions if MM minimization was also specified it is also performed at each QM step The next QM step takes into account the new MM atom distribution and energy terms If a single point QM calculation is selected the current QM MM energy is calcu lated without MM minimization The speed of QSite is largely determined by the size of the QM region Therefore there is no advantage to making a smaller model protein However please note that the s huge Impact executable option needed for systems with more than 8000 atoms or 8000 bonds is not available for QSite jobs Cartesian constraints may be placed on atoms in both the QM and the MM regions See Section 7 8 on page 130 for a brief description of the two types of constraints Frozen atom constraints can be applied to atoms in both regions Buffered atom constraints can be specified for MM region atoms but are ignored if applied to QM region atoms Note In general a QSite calculation can only be performed using a single entry If you want to run a QSite job using the Workspace structure as input and that structure includes multiple entries combine them into a single entry using the Merge option from the Entry menu in the Project Tabl
186. nd for energy minimization Energy Minimization Distance dependent dielectric constant 2 0 Maximum number of conjugate gradient steps 100 Final Scoring Reject pose unless Coulomb vdW score lt 0 0 Hydrogen bond score lt 0 0 Metal ligand score lt 0 0 Start Write Job Files Hide Help Figure 6 9 The Scoring folder of the Glide panel FirstDiscovery 3 0 User Manual 87 Chapter 6 Glide 6 6 1 Refinement of Initial Poses Section The Refinement of initial poses on coarse grid section of the Scoring folder tailors the way poses pass through the filters for the initial geometric and complementarity fit between the ligand and receptor molecules The grids for Stage 2 of the hierarchy contain values of a scoring function representing how favorable or unfavorable it would be to place ligand atoms of specified general types in given elementary cubes of the grid These grids have a constant spacing of 1 A The rough score for a given pose of the ligand relative to the receptor is simply the sum of the appropriate grid scores for each of its atoms Negative scores are favorable so the lower more negative the better The initial rough scoring is done on the coarse grid on which the possible positions for placing the ligand center are separated by 2 A twice the elementary cube spacing in X Y and Z The refinement step rescores the successful rough score poses after the
187. nd which forces will be treated as long range that is updated every n steps as specified in the previous option and estimated between updates 7 8 The Constraints Folder The Constraints folder includes selection options that allow regions of the receptor to be defined as frozen or buffered This folder is similar to the Constraints folder in the Impact Energy Minimization panel Control settings that do not apply to Liaison simulations are omitted If the Analysis folder is open you must first go back to the Settings folder and select Simu late for the Job type The selection options are described below Liaison Job fit sim Login saunders Host localhost 1 Settings System Parameters Constraints Analysis Frozen Atoms Buffered Atoms Start Write Job Files Hide Help Figure 7 5 The Constraints folder of the Liaison panel 130 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Frozen Atoms Liaison simulations can be performed with some atoms frozen so that they never move from their initial position during minimization or dynamics Clicking this button opens the Frozen Atoms panel which selects atoms of the receptor to be treated as frozen The atoms or atom sets can be chosen by picking atoms residues or molecules from the Workspace or by using the Atom Selection dialog box ASD See Chapter 2 the Maestro User Manual or the Maestro online help for information o
188. ne Job type This pair of buttons determines the type of Liaison job to be run Simulate Use this selection to set up a Liaison simulation It allows access to all Liaison folders System Parameters and Constraints except for the Analysis folder Analyze results of earlier simulations Use this selection to analyze the output of completed Liaison simulations by fitting calcu lated results to empirical binding energy values or by predicting the binding energy of new ligands This selection deactivates the System Parameters and Constraints folders and activates the Analysis folder Number of processors to use Liaison simulation jobs can take advantage of multiple processors to perform distributed processing Use this text box to specify the number of processors on which to run concur rent Liaison simulations For example if there are 10 ligand receptor combinations for a total of 20 jobs 10 free and 10 bound and there are 8 processors setting this number to 4 will launch 4 jobs when you click the Start button On each processor when one job completes another job will start until all simulations have been submitted Note this option indicates how many processors on the same machine to run simulta neously it is meaningless when jobs are submitted to a batch queue where each of the ligands is independently queued This option is not available when the Job type is Analyze results of earlier simulations as analy
189. nel in Maestro and each of its folders including instructions for using Glide constraints Glide similarity and extra precision Glide docking Glide XP A description of the Glide Pose Viewer panel e A usage summary for Glide utilities including para_glide which permits distrib uted processing for docking large sets of ligands For more information on the technical aspects of Glide and on its performance and results see the FirstDiscovery Technical Notes For a tutorial on using Glide see the FirstDis covery Quick Start Guide Much of the information in this chapter is available in the Maestro online help 6 1 Introduction to Glide Glide uses a hierarchical series of filters to search for possible locations of the ligand in the active site region of the receptor The shape and properties of the receptor are repre sented on a grid by several different sets of fields that provide progressively more accurate scoring of the ligand poses A pose is a complete specification of the ligand its position and orientation Conformational flexibility is handled in Glide via an extensive conformational search augmented by a heuristic screen that rapidly eliminates conformations deemed unsuitable for binding to a receptor such as conformations that have long range internal hydrogen bonds As illustrated in Figure 6 1 on page 66 each ligand is divided into a core region and some number of rotamer groups Each rotamer group is attached to the
190. neutralized before ionization states can be generated Neu tral molecules are also required by various applications such as QikProp The neutralization is performed by neutralizer which adds or removes hydrogen atoms 6 Generate ionization states For some applications it is important that all species that exist in a given pH range are available In this step the ionizer generates various ionization states for each structure This step should be preceded by a neutralization step 7 Generate tautomers As with ionization the significantly populated tautomers may be important for some types of calculations such as docking with Glide The tautomerizer generates various tautomers for each structure 8 Filter structures In this step structures that match specified conditions can be removed The condi tion can be on a property such as Molecular weight gt 1000 or on the structure such as the presence or absence of a specific functional group This step is per formed by ligparse 9 Generate alternative chiralities 2D structures do not always have complete chirality information and it can be use ful to vary the chiralities of the atoms to find all the low energy structures or to provide a range of possible structures for investigation This step identifies addi tional chiral atoms in the structures and generates additional structures with the same molecular formula but different chiral properties The step is performed by th
191. ng glide sort yourself is useful in a number of situations If you decide after the output file has been produced to sort poses using different criteria you can run glide sort with different settings on your output job name lib mae or jobname _pv mae file If you want to use a custom scoring function you can specify it by setting coeffi cients for the component energy scores creating a new composite scoring function If Glide stops unexpectedly you can run glide sort on the jobname raw mae file to recover all relevant data generated to that point f you want an assessment of progress made so far you can run glide sort on the jobname raw mae file at any time during the docking run In rigid docking runs there is no jobname raw mae file produced Therefore glide sort cannot be used to recover structures that were rejected during the docking calculation It is still possible to whittle down the jobname rept file further by using glide sort on the output mae file instead if you want to apply stricter criteria for saving poses than in the original run For in place scoring there is no structure output file since the input structures are not altered Instead of the rept file a scor file is produced containing scoring informa tion for the input structure FirstDiscovery 3 0 User Manual 93 Chapter 6 Glide 6 8 The Constraints Folder The Constraints folder is used to set up docking constraints receptor ligand h
192. nto near and far compo nents the forces that are computed explicitly from Coulomb s Law rather than from the multipole expansions This setting is relevant only when the Reversible RESPA integrator is used with more than two stages See Section 10 4 on page 167 9 4 5 The Periodic Boundary Conditions Panel Impact calculations can be performed with periodic boundary conditions This technique is usually applied with explicit solvent in order to avoid nonphysical edge effects The system of interest is defined to be in a box of a given size images of which are replicated throughout space to form an infinite 3D lattice To open the Periodic Boundary Conditions panel select Use periodic boundary conditions then click Settings The selection options of the Periodic Boundary Conditions panel are Box X Y and Z lengths Use these three text boxes to set the size of the simulation box The minimum size for any dimension that Maestro will use is 18 62 A 158 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization Use Ewald long range correction Click to select the Ewald summation method for efficiently summing long distance elec trostatic interactions in periodic systems Unlike the Fast Multipole Method Ewald does not require the net charge of the system to be zero This setting is ignored when the Fast Multipole Method is used Maximum length of K space vectors The value in this text box is used to determine the n
193. nu equiva lents are listed in Table 2 2 FirstDiscovery 3 0 User Manual 11 Chapter 2 Introduction to Maestro Table 2 2 Shortcut keys in the Maestro main window Keys Action Equivalent Menu Choices ALT B Show Build panel Edit gt Build ALT C Create entry Project gt Create Entry From Workspace ALT E Show Command Script Editor panel Edit gt Command Script Editor ALT F Open Find Atoms panel Edit gt Find ALT H Show Help panel Help gt Help ALT I Show Import panel Project Import Structures ALT M Show Measurements panel Tools gt Measurements ALT N New project Project gt New ALT O Open project Project gt Open ALT P Print Maestro gt Print ALT Q Quit Maestro gt Quit ALT S Show Sets panel Tools gt Sets ALT T Show Project Table panel Project gt Show Table ALT W Close project Project Close ALT Z Undo Redo last command Edit gt Undo Redo 2 4 Maestro Projects All the work you do in Maestro is done within a project A project consists of a set of entries each of which contains one or more chemical structures and their associated data In any Maestro session there can be only one Maestro project open If you do not specify a project when you start Maestro a scratch project is created You can work in a scratch project without saving it but you must save it in order to use it in future sessions Maestro also creates a scratch project when you close a project Likewise if there is no entry displaye
194. o FirstDiscovery 3 0 User Manual 23 Chapter 2 Introduction to Maestro Preferences prefer Bex Delete Markers Font Size Project Directory Label Mouse File suffix Builder Default directory for job startup and file i o Maestro s current working directory ww Parent of project directory w Project directory vy Project jobs directory ww Other specify below Directory currentdir Figure 2 6 The Directory folder of the Preferences panel 2 9 Undoing an Operation To undo a single operation click the Undo button in the toolbar choose Undo from the Edit menu or press ALT Z The word Undo in the menu is followed by text that describes the operation or operations to undo Not all operations can be undone for example global rotations and translations are not undoable operations For such operations you can use the Save view and Restore view buttons in the toolbar which save and restore a molecular orientation If you think that you might want to undo a series of operations later you can start an undo block by selecting Begin Undo Block from the Edit menu When you have completed the group of operations you want to undo end the block by selecting End Undo Block from the Edit menu Then to undo the operations in the block choose Undo from the Edit menu Undo is not supported for all Maestro operations An undo block can be created only if at least one undoable operation has been performed since
195. o Ligands with similarities between 0 30 and 0 70 will be partially penalized Start Write Job Files Hide Help Figure 6 13 The Similarity folder Use similarity score in docking 102 FirstDiscovery 3 0 User Manual Chapter 6 Glide No penalty for ligands with similarity gt The value entered here is the similarity threshold Snax above which ligands get no penalty or reward This is a real number between 0 0 and 1 0 with a default of 0 7 and must be less than or equal to the Full Penalty threshold in the previous item Reject ligands with similarity lt ____ This must be a positive number between 0 0 and 1 0 The default is 0 0 Glide will skip any ligand whose maximum similarity to any of the actives is less than this value Thus the default value of 0 0 means do not skip any ligands while the maximum value of 1 0 means skip any ligand that is not identical to or a stereoisomer of one of the known actives 6 10 The Pose Viewer The Pose Viewer is not part of the Glide panel but has its own panel which you open from the Tools menu Use the Glide Pose Viewer panel to display the contents of a Pose Viewer file written by Glide and to write out selected poses to another file To open the Pose Viewer choose Glide Pose Viewer from the Tools menu 6 10 1 Pose Viewer Panel Features File Selection Click Open to display a file selector Use this selector to choose a pose file to display Such fil
196. o draw with default C Each click in the Workspace places an atom and connects it to the previ ous atom Delete Choose an object to delete Menu button with a pick menu and other items Same as the Delete button on the main toolbar Set element Pick atoms to change to the selected element default C Menu button with a list of target elements Menu button with a limited list of target elements Increment bond order Pick a bond to increase its bond order by one to a maximum of 3 Decrement bond order Pick a bond to decrease its bond order by one to a minimum of 0 Increment formal charge Pick an atom to increase its formal charge by one Decrement formal charge Pick an atom to decrease its formal charge by one Move Pick an atom to move in the xy plane or the z direction Menu button with a list of direc tions Moves in the xy plane are made by clicking the new location Moves in the z direc tion are made in 0 5 A increments Label Apply heteroatom labels as you build a structure The label consists of the element name and formal charge and is applied to atoms other than C and H Display Connect Fuse panel Open the Connect amp Fuse panel so you can connect structures create bonds between structures or fuse structures replace atoms of one structure with those of another Display Adjust panel Open the Adjust panel so you can change bond lengths bond angles dihedral angles or atom chiralities Add hydrogens
197. on SCHRODINGER protprep options input file or the pprep and impref utilities See Section 4 11 on page 55 for more information about command line protein preparation 3 4 2 Glide Using Maestro is the best way to write Glide job scripts even if you intend to run them from the command line The scripts are very intricate and are subject to change with each new distribution of the program To run a Glide job script enter S SCHRODINGER impact i jobname inp o logfile By default the log information is written to jobname 1log but if you want to use a different file name use the o option If your protein has more than 8000 atoms and you are making grid files but not if you are just docking ligands you will also need to include the s huge switch in the command The para glide utility can be used to launch a large Glide docking job distributing the ligand database over a number of processors See Section 6 11 on page 107 for more infor mation While Maestro provides the Pose Viewer interface to visualize high scoring poses you can also see the numerical results for these poses in the jobname rept output file A score in place calculation writes a jobname scor report file instead and no structural output for the Pose Viewer These results are retained as Maestro properties in the Pose Viewer file jobname pv mae or ligand database file jobname 1ib mae and can be displayed in the Maestro Project Table 32 First
198. on input file for simulation of the ligand receptor complex Link to the receptor structure file jobname mae that Maestro wrote in the Maestro working directory In a single ligand job the ligand is also contained in the structure file if it was taken from the Workspace Link to the location of the ligand file which may or may not be the same as the receptor structure file jobname lig min mae Final minimization structure for the ligand from the bound simulation when minimization is used as the sampling method or when the ligand is minimized prior to Hybrid Monte Carlo or Molecular Dynamics sampling jobname rec min mae Final minimization structure for the receptor from the FirstDiscovery 3 0 User Manual Chapter 7 Liaison bound simulation when minimization is used as the sampling method or when the complex is minimized prior to HMC or MD sampling jobname lig fin mae Final simulation structure for the ligand from the bound simulation when HMC or MD sampling is used e jobname rec fin mae Final simulation structure for the receptor from the bound simulation when HMC or MD sampling is used e Other output files from the simulations including energy output out 1log ave and trajectory files from sampling trj An example Liaison directory structure for a Multiple Ligand Single Receptor job named 1bkm is shown below home user ls 1bkm simulate 1bkm 1bkm mae ls 1bkm l1bkm 3m 1 l1bkm 3m 2
199. onserve energy will lead to an unstable MD simulation Constant pressure NPT For this ensemble both temperature and pressure are held constant during the simulation This is accomplished by also coupling the system to a pressure bath using the algorithm of Berendsen et al J Chem Phys 1984 81 3684 Seven settings become available when this ensemble type is chosen Target temperature The same as for the Constant temperature ensemble Temperature relaxation time The same as for the Constant temperature ensemble Target pressure This text box specifies the desired pressure in atmospheres The actual pressure will fluctuate about the desired value At each MD step the system FirstDiscovery 3 0 User Manual 171 Chapter 10 Molecular Dynamics Simulations will be scaled such that the pressure will approach the desired value on a timescale determined by the Volume Relaxation Time parameter described below The default pressure value is 1 atm The acceptable range is any positive or negative real value Volume relaxation time This text box sets the volume relaxation time in picoseconds for volume scaling in a constant pressure MD simulation The default value is 0 01 ps The acceptable range is any value greater than zero e Solvent isothermal compressibility text box Isothermal compressibility or x V dV dP in units of atm is the pressure analogue of the heat capacity and relates to the tendency of the solvent s volu
200. or and a ligand are displayed in the Workspace and the ligand has been identified Selecting this option sizes the enclosing box to fit the longest dimension of the displayed ligand plus the bounding box This option is only appropriate if the ligands to be docked are of the same or smaller size than the displayed ligand The Fit ligands with length lt n A option fits the enclosing box to ligands with the maximum length specified in the text box The default maximum ligand length is 20 This option is appropriate when you know the maximum ligand size in the input file or the maximum size to be considered or when you want to apply a spe cific restriction on the region within the active site in which any docked ligand must lie Scaling of vdW radii for nonpolar receptor atoms Glide does not allow for flexible receptor docking for Glide Prime induced fit docking see Section 6 1 3 and the Prime documentation but scaling of van der Waals radii of nonpolar atoms which decreases penalties for close contacts can be used to model a slight give in the receptor and or ligand The options for scaling nonpolar receptor atoms are e Scale radius if Ipartial atomic chargel lt n Scaling of van der Waals radii is performed only on nonpolar atoms defined as those for which the absolute value of the partial atomic charge is less than or equal to n The value entered for n must be a positive number The default for atoms in the receptor
201. or the job from the Host option menu If you use a different login on the remote host you have selected enter that login in the Login text box 4 9 2 Defining the Ligand Before launching a protein preparation job you must choose a molecule in the Workspace that will be treated as the ligand In the ProteinPrep panel choose Pick and then select the ligand by clicking on it in the Workspace When Show markers is chosen the ligand will be highlighted with a blue green marker The rest of the Workspace is then treated as the protein 4 9 3 Choosing a Procedure The ProteinPrep panel facilitates three types of jobs Preparation only Refinement only and Preparation and refinement The Preparation component neutralizes residues that are beyond a set distance from the ligand The Preparation process also detects some conflicts in hydrogen bonding It corrects them when possible either by exchanging carbonyl and hydroxyl oxygens in a neutralized carboxylic acid group or by creating the alternate HIE tautomer of a histi dine side chain The Refinement component uses Impact to run a series of restrained partial minimizations on the combined hydrogenated structure Minimizations continue until the average RMS deviation of the non hydrogen atoms reaches the specified limit 0 3 A by default The first step in the sequence of restrained minimizations reorients side chain hydroxyls in serine threonine and tyrosine residues and side chain
202. orrect job performance 3 1 3 Reasons to Run Jobs from the Command Line Although you will normally set up FirstDiscovery jobs using the controls and settings in the Maestro GUI you can submit jobs either from within Maestro or from the command line You sometimes might want to submit jobs from the command line for the following reasons The command line scripts can run all full featured jobs written using the FirstDis covery and Impact panels in Maestro and also allow you to override specific run time values that are not accessible through the Maestro interface Command line scripts allow you to run FirstDiscovery jobs when you want Command line scripts can be modified and jobs can be re run without reconfiguring and reloading job settings in Maestro FirstDiscovery 3 0 User Manual 27 Chapter 3 FirstDiscovery from the Command Line Some job options such as trajectory file analysis are available only when you run Impact from the command line The Write Job Files button in various Maestro panels writes the input files needed for a job See Section 3 4 on page 31 for more information 3 1 4 Force Fields and Write Template The molecular mechanics force field for Basic Impact applications and for Glide and Liaison in FirstDiscovery 3 0 is the OPLS2001 version of OPLS AA OPLS2001 is designed to work with automatic atom typing and is incompatible with template mode If you attempt to write a template file Impact command
203. ose file during the docking calculation The raw in the file name indicates that these poses have not been sorted by score The jobname raw mae file has the same format as the jobname lib mae or 92 FirstDiscovery 3 0 User Manual Chapter 6 Glide jobname pv mae file This file contains all poses that qualify for inclusion in the final report i e subject to the Keep at most specifications at the current stage of the calcula tion At the successful conclusion of a flexible docking job Glide invokes the g1ide sort utility This utility filters the overcomplete structure set in the raw pose file using the Final Output filters from the Scoring folder see Section 6 6 on page 86 and the duplicate poses filter from the Output folder It then sorts the filtered poses by score the default is to sort using the GlideScore to produce the output pose file either jobname lib mae or jobname pv mae A report file jobname rept is also written The default g1ide sort settings usually suffice to produce a sorted and filtered output file containing all the useful poses that were in the raw file Once the output file has been written the jobname raw mae file can be deleted to save space You can also run glide sort from the command line either during or after a Glide docking job on raw or output pose files Like other Glide utilities glide sort is installed in your SCHRODINGER utilities directory See Section 6 11 for a usage summary Runni
204. ounding box Enclosing boxes that are larger than this are not useful they take up more space on disk and in memory for the scoring grids which take longer to compute The ligand center is defined in a rigid docking run as the midpoint of the line drawn between the two most widely separated atoms The definition changes slightly for flexible docking where the ligand center becomes the midpoint between the two most widely separated atoms of the core region the part of the ligand remaining after each of the end groups has been stripped off at the outward end of the connecting rotatable bond The two boxes share a common center Thus the operations in the folder that center one box also center the other Each rigidly docked ligand or flexibly docked conformation has an associated length L which can be defined as twice the distance from the ligand center to the farthest atom The required relationship between L and the lengths E and B of the enclosing and bounding boxes for successful placement of the ligand center anywhere within the bounding box is E2B L The enclosing box must be large enough in each dimension to hold the length of the bounding box plus the maximum length of any ligand If a larger ligand is encountered not all positions for the center of the ligand in the bounding box are accessible The effec tive bounding box for that ligand will be smaller than the dimension nominally specified Glide restricts the size of
205. ove or modify these options as appropriate See the Jaguar User Manual for more information on these keywords Number of processors to run job The QM Jaguar portion of the QSite job can be run in parallel if multiple processors are available Use of this option requires a license for parallel Jaguar Specify the number of computer processors that will be used for the QM calculation Do not use parallel processing for jobs where solvation is selected Use continuum solva tion in the QSite Potential folder See Section 8 3 148 FirstDiscovery 3 0 User Manual Chapter 8 QSite GM Residue Ligand iqmres Exi 21 0 W Show markers 1 W Residue selection by backbone picking j 1 r i i Residue selection by sidechain picking i j 1 I I J Free ligands Basis set 6 31G Delete Figure 8 6 The QM Residues Ligands panel in QSite QM regions These options allow you to define the QM region Residues Ligands This button opens the QM Residues Ligands panel which is used to define and add resi dues to the QM region see Section 8 7 2 lons This button opens the QM lons panel which is used to add atoms typically ions to the QM region see Section 8 7 3 8 7 2 The QM Residues Ligands Panel The QM Residue Ligand panel is used to select and add protein residues or non covalently bound ligands to the QM region The features of the QSite Residue Ligand panel are List of QM region re
206. pace Enhance depth cues Optimize fogging and other depth cues based on what is in the Workspace Rotate around Y axis by 90 degrees Chapter 2 Introduction to Maestro Tile entries Arrange entries in a rectangular grid in the Workspace Save view Save the current view of the Workspace orientation location and zoom Display only picked atoms Pick atoms to display Menu button with a pick menu Also display Add the selected atoms to the display Menu button with a list of predefined atom categories and an item to open the Atom Selection dialog box Display residues within N angstroms of currently displayed atoms Menu button with a list of values and an item to open a dialog box to set a value Draw bonds in wire Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Draw atoms in ball and stick Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Color all atoms by scheme Menu button with a list of schemes Label atoms Label all atoms with the selected label Menu button with a list of label types and an item to delete labels 10 A amp P Reset workspace Reset the rotation translation and zoom of the Workspace to the default state Restore view Restore the last saved view of the Work space orientation location and zoom Display only Display only the selected a
207. pact These methods account for the effects of solvent without the use of explicit water molecules 156 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization 9 4 3 The Truncation Panel The Truncation panel defines the truncation settings for an Impact calculation When suffi cient care is taken the use of truncation to remove interactions between widely separated pairs of atoms is an important strategy for reducing the time and memory required to perform calculations on large systems Currently only residue based cutoffs are supported for calculations set up by Maestro This means that all atoms within complete residues that have any pair of atoms within the cutoff distance will be included in the nonbonded inter action list To open the Truncation panel select the Use truncation option and click the adjacent Settings button The selection options in the Truncation panel are Update neighbor list frequency When truncation is active all the pairs that fall within the cutoff radius are stored in a neighbor list During a minimization calculation or a dynamics simulation the geometry of the structure may change so as to bring some pairs of atoms that were originally outside the cutoff distance to within the cutoff Conversely some pairs of atoms may move outside the cutoff distance For these reasons the neighbor list needs to be updated from time to time The frequency of this update is controlled by this integer field By
208. prex lette pete 70 6 3 Whe Settings EOldeE xe eerte irre epe FeESek asa E E RORIS U Cd pd 70 6 3 1 Glide Function Set Up Grids or Dock Ligands sss 70 6 3 2 Docking Mode Options and Using Extra Precision Mode 71 6 3 3 Other Settings Folder Options ccccesceesceseeeseeeeeeeeeeeeeeeeaeeeeeeseeeeeeees 72 6 4 The Site Polder esis cene crier adbahacdaaessseuedeab sites sages ees te Eee padece s feciuta 74 6 4 1 Site Folder Features ccccssccssscsssecsssesssecsssessseesseesssecsscesnsecsseesseeesees 75 6 4 2 The Ligand to Define Grid Panel eee 78 6 4 3 The Active Site Residues Panel eessseseeeeeeenenn 79 6 5 Whe Lipand Foldet srodni er nd repete HP re es 80 6 5 1 Ligand Folder Eeatutes o otio e elsi tO PER 80 6 5 2 The Reference Ligand Panel aee re Hence e teint 85 FirstDiscovery 3 0 User Manual v Contents 6 6 The Scoring Polder iczscii csd sacessteriestaeesteeianaacassiaivsadearatedethaeseelieans 86 6 6 1 Refinement of Initial Poses Section sse 88 6 6 2 Energy Minimization Section essere 89 6 6 3 Binal Scoring Sets tiere rere eret Ene eoe hdd eee be eee bia is 89 6 7 Lhe Output Polit ione erp ee tiet ere dece etie ever ice eine oE 90 6 7 1 Elimination of Duplicate Poses Section sse 90 6 7 2 Structure Output Section essere 91 6 7 3 Raw Pose File
209. ra g1ide script which creates and if speci fied submits for distributed processing several smaller subjobs covering the range of ligands in the starting template file you specify The para glide script is installed in the SSCHRODINGER utilities directory see the usage summary on page 110 Also see the First Discovery Technical Notes for more details 82 FirstDiscovery 3 0 User Manual Chapter 6 Glide Other uses for range bounds settings To dock all structures from the first range value to the end of the file set the To value to 0 If the first value is 1 and the second value is 0 all structures in the file will be docked Note The To second value should never be less than the from first value except when To is set to 0 Note Neither value can be less than zero n the event that a problem with Glide or with the input ligand causes a submitted Glide job to terminate abnormally you can set these range bounds to pick up after the point in the input ligand file at which the problem occurred Docking scoring mode The docking scoring modes are Generate conformations for each input structure flexible docking Dock each input structure rigidly Score each input structure in place scoring output file jobname scor These options determine whether input ligands are to be docked flexibly rigidly or not at all evaluated and scored in place For flexible docking the options here further deter mine wheth
210. rch begins with the selection of site points on an equally spaced 2 A grid that perme ates the active site region Stage 1 in Figure 6 2 on page 67 To make this selection pre computed distances from the site point to the receptor surface evaluated at a series of pre specified directions and binned in 1 A ranges are compared to binned distances from the ligand center the midpoint of the two most widely separated atoms to the ligand surface Glide positions the ligand center at the site point if there is a good enough match but skips over the site point if there is not The second stage of the hierarchy begins by examining the placement of atoms that lie within a specified distance of the line drawn between the most widely separated atoms the ligand diameter This is done for a pre specified selection of possible orientations of the ligand diameter Step 2a If there are too many steric clashes with the receptor the orien tation is skipped Next Step 2b rotation about the ligand diameter is considered and the interactions of a subset consisting of all atoms capable of making hydrogen bonds or ligand metal interactions with the receptor are scored subset test If this score is good enough all interactions with the receptor are scored Step 2c The scoring in these three tests is carried out using Schr dinger s discretized version of the ChemScore empirical g Rotamer group P ud oO Rotamer group Figure 6
211. re information about structure editing in Maestro click Help or see the Maestro User Manual 48 FirstDiscovery 3 0 User Manual Chapter 4 Protein Preparation 4 8 Adjusting the Ligand 4 8 1 Adjusting Ligand Atom and Bond Properties If you have not already colored by element do so now Choose Element from the Color all atoms by scheme button menu amp To set or change ligand bond orders 1 If the Build panel is not displayed click Show Hide build panel on the main toolbar F 2 On the Build panel toolbar click the Decrement bond order or Increment bond order button as appropriate Cl GC 3 Click on bonds as necessary to set the bond order To set or change formal charges on any ligand atoms On the main toolbar choose Formal Charge from the Label atoms button menu Q E 2 If the Build panel is not displayed click Show Hide build panel on the main toolbar Ps 3 On the Build panel toolbar click on the Increment formal charge or Decrement formal charge button as appropriate amp 4 Click on an atom whose formal charge must be increased or decreased Repeat as necessary The atom labels show the current formal charge FirstDiscovery 3 0 User Manual 49 Chapter 4 Protein Preparation To correct the atom type of any mistyped atoms 1 On the main toolbar choose Atom Type MacroModel from the Label atoms button menu o 2 Ifthe Build panel is not displayed click Show Hide build pan
212. reis R S 141 148 SGB model teer 113 conventions document eeeeeeeee 2 convergence criteria esses 164 core conformations eeseseeeeeeeene 65 Core ligand cett ees 65 Coulomb energy eee 68 Coulomb van der Waals score 90 G trent energy enorme reno ees 89 current working directory 6 cutoff distance residue based 157 CUS EE DIEN backbone QSite side chain D database screening eee 68 desalter LigPrep utility 60 diameter ligand 66 dielectric constant se 155 distance dependent 155 setting value seen 156 directory current Working 6 23 FirstDiscovery eee 27 Impact crnac ie eitieieeeets 27 UE 27 uii M 23 structure Liaison 27 utilities ote meth 39 distance dependent dielectric 89 distributed processing 33 65 Ghde s Use eee eerie 32 82 110 L11S0n0 5c aee rond 121 136 docking extra precisioN scissa na 69 flexible 66 83 flexible receptor sess TI HP 1th 66 84 93 rigid receptor btts 69 SP mode 3 69 XP mode ense remet 69 182 docking mode 70 71 72 SP 69 OP PETERE 69 duplic
213. rigid translational repositioning of 1 0 or 1 A in X Y and Z that gives the repositioned ligand the best possible score This procedure effectively doubles the resolution of the scoring screen The three text boxes in this section are described below Keep ____ initial poses per ligand for refinement This text box sets the maximum number of poses per ligand to pass to the grid refinement calculation The default maximum number depends on the type of docking specified For flexible docking jobs in general the default is 5000 poses If Glide Constraints have been applied to a flexible docking job 500 poses e If extra precision XP docking has been selected the maximum number of poses is internally adjusted to a minimum of 800 For rigid docking the default is 1000 poses This number is not changed by the application of Glide Constraints You can change the default by entering any integer value greater than zero Scoring window for keeping initial poses This text box sets the rough score cutoff for keeping poses for refinement To survive the score of a given pose must be within the value entered of the best pose accumulated so far The default setting is 100 0 but you are allowed to choose any real value greater than zero Keep refined poses per ligand for energy minimization This value allows at most the number of poses specified per ligand to be energy minimized on the OPLS AA nonbonded interaction grid The
214. rop properties you can set up a filter and use it to select entries for the job If you save it you can use it again on a different set of ligands that met the same selection criteria You can create filters in the Entry Selection dialog box which you can open from the Select menu Only Add Deselect from the Edit Filter dialog box or by clicking the Entry selection button on the toolbar X FirstDiscovery 3 0 User Manual 15 Chapter 2 Introduction to Maestro To create a filter choose a property from the property list choose a condition and combine it with the current filter by clicking Add Subtract or Intersect These buttons perform the Boolean operations OR AND NOT and AND on the corresponding ESL expressions Once you have created a filter you can click OK to apply it immediately or name and save it for later use 2 4 4 Including Entries in the Workspace In addition to selecting entries for various tasks you also control which entries are displayed in the Workspace from the Project Table An entry that is displayed in the Work space is said to be included in the Workspace likewise an entry that is not displayed is excluded Included entries are marked by an X in the diamond in the In column excluded entries are marked by an empty diamond Entry inclusion is completely independent of entry selection To include or exclude entries you can click shift click and control click in the In column or select entries and t
215. rt from a terminal window You can define SCHRODINGER as follows csh tcsh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory Entering 1s SSCHRODINGER at the command prompt will list the Schr dinger installa tion directory contents including the Maestro startup script maestro and the Impact startup script impact Unless otherwise specified Schr dinger applications and utilities run under a job control system and are automatically backgrounded You need not add an amp at the end of the commands to have them run and immediately return your command prompt The WAIT option of the impact command prevents automatic backgrounding so you can embed such commands in other scripts FirstDiscovery 3 0 User Manual 31 Chapter 3 FirstDiscovery from the Command Line impact s size If this option is unspecified Impact guesses which executable to use based on molecular size values given in the command input file As a rule of thumb the s huge option should be used on systems of greater than 8000 atoms or 8000 bonds However even on large systems Glide jobs that dock ligands using previously written grid files rather than computing grids from a receptor structure do not require the s huge option Note the s huge option cannot be used with QSite jobs 3 4 1 Protein Preparation Protein preparation jobs can be run from the command line using the protprep applica ti
216. ruct log The log file for the complete preparation and refinement job 4 10 Checking the Output Structures Finally after both the preparation and refinement components have successfully run you should check the completed ligand and protein structures 4 10 1 Checking the Orientation of Water Molecules Perform this step only if you identified and kept some structural waters in Section 4 5 Reorienting the hydrogens is not strictly necessary as their orientation should have been changed during refinement in Section 4 9 but it is useful to check that the orientation is correct If the orientation is incorrect reorient the molecules by using the following procedure On the toolbar choose Global Local from the Local transformation button menu L3 El The Advanced Transformations panel is displayed 2 Under Atoms For Transformation use the picking controls to select the entire water molecule you want to reorient 3 Under A Center For Transformation use the picking controls to select the oxygen atom of the water molecule 4 Under Rotation Translation Scope select Local 5 Use the middle mouse button to change the orientation of the water hydrogens 6 Hide the Advanced Transformations panel Transformations should now be global again When you have corrected the orientation of the retained water molecules run a Refine ment only job on the adjusted protein ligand complex as described in Section 4 9 54 FirstDisco
217. ry 3 0 User Manual Chapter 13 Getting Help For help installing and setting up licenses for Schr dinger software see the Schr dinger Product Installation Guide The Maestro help facility consists of Auto Help Balloon help tooltips and online help To get help follow the steps below Check the Auto Help window located below the title bar of the main window If help is available for the task you are performing it is automatically displayed there If your question concerns an interface element e g a button or option menu there may be Balloon help for the item Move the mouse pointer over the element If there is Balloon help for the element it appears within a few seconds If you do not find the help you need using the steps above click the Help button in the panel for whose settings you are seeking help The Help panel is opened and a relevant help topic is displayed For help with a concept or action not associated with a panel open the Help panel from the Help menu on the main menu bar or by using the key combination ALT H If you do not find the information you need in the Maestro help system check the following sources The Maestro User Manual for questions about Maestro The FirstDiscovery Technical Notes for information about technical or scientific issues The Maestro Release Notes The FirstDiscovery Release Notes The Frequently Asked Questions page located at http www schrodinger com Support fags html
218. ry 3 0 User Manual Chapter 8 QSite QSite qsite Job gsitetmp Login dyal Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries lt gt Replacing existing entries lt gt Do not incorporate Potential Constraints Minimization Optimization QM Settings Optimization options for the QM region Method Transition state Maximum number of iterations 100 TS method QST c Reactant entry Product entry TS guess entry 0 50 Fraction of palh between rmeactant and product Start Write Job Files Hide Help Figure 8 4 The Optimization folder with TS method QST selected These initial guess structures can be selected items in the Workspace or specified entries in the Project Table The Optimization folder includes the following menus and options Method The Method menu controls the OM calculation type The options are Single point default Minimization Transition state If you choose to run a Single point calculation the QM energy is calculated for the struc ture as it stands No QM geometry optimization or MM minimization is performed and the settings in the Minimization folder are ignored The other features in the Optimization folder are not needed and are dimmed go on the QM Settings folder Choose Minimization to locate a minimum energy structure by geometry optimizatio
219. s Output Pose Files and glide sort 92 6 5 The Constraints Folder oio mo ICE OE RURSUS ERES 94 6 8 1 Using Glide Constraints eec eerte eee e ree e Pee RN TH 94 6 8 2 Glide Constraints Folder Features Grid Generation 95 6 8 3 Glide Constraints Folder Features Docking ss 97 69 The Similarity Polder o oerte oder tectae taret ert i decem 98 6 9 1 Introduction to Similarity Scoring in Glide sss 98 6 9 2 Similarity Folder Features Grid Generation sss 99 6 9 3 Similarity Folder Features Docking esee 101 6 10 The POSE VIE WEE ien teret irre rr E RRD GR ee ole de eigen 103 6 10 1 Pose Viewer Panel Features esses 103 6 10 2 Th Pose Write Paiel 0 eet re ree ea ete tpe it tit nere Ep EEEE eran 107 6 11 Glide Utilities 2 arr erect cose cas retener ER Ee t terree eerie eigen 107 6L 1 1 ep elei OS OE Bods uds opcra ren Ou dH dicere ereg 108 611 2 glide rescore uuu nom IDEO IRE HERE SIEHE 109 6113 para p DO secos motion OU WR EDO TESTO 110 Chapter 7 EI3IS0H eteet eere eoo teee eet ete poene respete ee Uer eese aa 113 T1 Brief Description of Liaison 5 eSI Enea enia 113 C2 MAGS OMS TMG ENAT E TERT OO TETTE 114 7 2 1 Liaison Directory SUC WES siiani te ea aaret iia 114 7 2 2 Directori s Created o ettet E aE dinge e pode 114 T29 Tales CEreateil ueteri pl
220. s and export structures and properties from entries in various formats 2 4 1 The Project Table Toolbar The Project Table toolbar contains two groups of buttons and a status display The first set of buttons opens various panels that allow you to perform functions on the entries in the Project Table The second set of buttons controls the ePlayer which plays through the selected structures each structure is displayed in the Workspace in sequence at a given time interval See Section 2 3 2 on page 8 for a description of the types of toolbar buttons The buttons are described below Project Table table test Table Select Entry Property ePlayer n A Sel Bol of R 414 41m 2 selected eooo mol0004 im fo jo Jo fo jo f Qo mol 0004 mol o004 imp1 incijo o O0 fo o f do mol 0007 mol 0007 im 2 amp o o jo jo p 4 mo _0007 Q mol_ooos mol_ooos impt inet o fo jo fo fo 0 0 o o mol 0018 Hidd Included Excluded Fixed or locked Selected entry entry entry entries Figure 2 2 The Project Table panel FirstDiscovery 3 0 User Manual 13 Chapter 2 Introduction to Maestro 14 Find Open the Find panel for locating alphanumeric text in any column of the Project Table except for the row number Sort Open the Sort panel for sorting entries by up to three properties Plot Open the Plot panel for plotting entry properties Import struct
221. s on a system composed of multiple entries 1 Include only those entries in the Workspace 2 Select Workspace as the Source of job input 11 2 Impact Hybrid Monte Carlo Panel Features The Impact Hybrid Monte Carlo panel has four tabbed folders Potential Constraints MD Parameters HybridMC FirstDiscovery 3 0 User Manual 173 Chapter 11 Hybrid Monte Carlo Simulations The Potential and Constraints folders are described in Chapter 9 Additional features of the Constraints folder appear in Section 10 3 on page 166 Features of the MD Parameters folder relevant to both Impact Dynamics and Impact HMC are discussed in Section 10 4 on page 167 The HybridMC folder is discussed in the next section 11 3 The Hybrid MC Folder The HybridMC folder defines the basic settings of the HMC task The selection options are Number of HMC cycles This text box sets the number of HMC cycles for the simulation The default value is 100 The acceptable range is any number greater than zero MD steps per HMC cycle This text box sets the number of MD steps per HMC cycle for the simulation The default value is 4 The acceptable range is any value greater than zero Liaison calculations use 5 MD steps per HMC cycle Impact Hybrid Monte Carlo ihmc Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries Replac
222. sef 8e c ve SOK LH s eef fersi s z feat nef s e PEL soif L1 s 3ce eee jose ope ece oj v 0 0 0 pueri ef 8 of s s8 osos gree j see serf e 2 ve IHS e se see foros se amp e eef os e 0 0 ZI Wtf 2 eef ois ferre Jeze v 3 o pur of of eef X see i zee Jerze sce ee se e pPuwebiL eid L 2 vez e s es s ce feere esj zt puebiL LOH E vipa AEn mpa pea Mps poon puaH fb1su lepow 3 6109S D ssod W guos aep enuf kepr fejdsig mt 08403d8252 4 403da2au aew ad 7uab juo 4 0p apL b e L103n3 Le L103n 484025 L0354 LJ uo Lyequawnzog suapunes awoy sayy 92 iuc spuog H sasod FirstDiscovery 3 0 User Manual 104 Chapter 6 Glide Ligand Pose Scroll List This part of the panel lists all of the ligand poses reported by Glide The entries are listed with a numerical index a title and various properties of the combination of the posed ligand and the receptor The index is the ligand s position relative to other ligands in the pose file Note that the first indexed ligand is actually the second structure in the file since the first structure is the receptor The Title field shows text that typically is a descriptive name or registry identifier for the ligand This 30 character field is carried over from the title or molecule name record of the input Maestro or MDL SD
223. sidues The text area at the top of the panel displays the list of QM residues as it is being constructed Note that Maestro assigns a residue number to every part of the input system Thus residue may refer to either an amino acid residue in the protein or to a free ligand or ion or solvent molecule FirstDiscovery 3 0 User Manual 149 Chapter 8 QSite Show markers If Show markers is selected a red trace highlights all of the residues selected for the QM region Any residue that is part of the QM region will also have its chain name molecule number residue number and insertion code if applicable included in the list at the top of the panel The QM Residue Ligand panel supports the following three methods for defining the QM region Residue selection by backbone picking Residue selection by sidechain picking Free ligands The first two methods are used to select amino acid residues or side chains These methods place cuts across bonds to alpha carbon atoms in the protein backbone and these cuts define the QM MM boundary The third method Free ligands previously called Ligand residue selection is used for non covalently bound structures such as solvent molecules or free ligands No cuts are made by this method To select residues for inclusion in the QM region by backbone picking Click Residue selection by backbone picking 2 Cuts must be made at the beginning and end of the OM region To do this pick any
224. sis jobs are much faster than simulation jobs FirstDiscovery 3 0 User Manual 121 Chapter 7 Liaison 7 6 The System Folder This folder sets the type of simulation to be run and defines the system and the source of the ligand or ligands to be used The key option is Simulation type and the options are Multiple ligands single receptor Single ligand single receptor Each option affects the selection options offered in the remainder of the panel These options are described below together with the selection options that pertain to each Selecting certain options dims other options that do not apply to the selected options For a Single ligand single receptor simulation you have two options Both receptor and ligand are loaded to the Workspace The structures do not have to be loaded in any particular order Only the receptor is loaded into the Workspace The ligand is defined via an external file Liaison Host localhost 1 Settings System Parameters Constraints Analysis Simulation type Multiple ligands single receptor Format of ligand files Maestro Source of ligand structures File containing a list of ligand names and associated structure files Filename Browse Mame ta use for Wis ligand Lig Start Write Job Files Hide Help Figure 7 3 The System folder of the Liaison panel 122 FirstDiscovery 3 0 User Manual Chapter 7 Liaison For
225. stics W Record trajectory Frames written every 5 J Sample velocities Start Write Job Files Hide Help Figure 10 2 The MD Parameters folder of the Impact Dynamics panel 168 FirstDiscovery 3 0 User Manual Chapter 10 Molecular Dynamics Simulations panel or in the Hybrid MC folder of the Impact Hybrid Monte Carlo panel Fast forces use the shorter time step computed by dividing the Time step by the integer entry in the text box Stop overall motion When this option is selected the default overall rotational and translational motion drift of the system is subtracted from the calculation Frequency of printing information This text box selects the frequency with which MD information is written during the simu lation The default value is to print information every 5 MD steps Any integer value greater than zero is allowed Collect MD statistics This option is off by default When it is selected the MD statistics are collected and are written to the end of the Impact output file These statistics measure fluctuations of the different energy terms Record trajectory This option is off by default When it is selected trajectory information is written to the file jobname trj in the Maestro working directory or for Liaison in the individual ligand directories arrayed under the Master Liaison Run Directory This information is written in binary format but can be analyzed using the ANALYSIS task of Impa
226. t Ligand Simulation Ligand Receptor Simulation Maximum minimization steps 500 RMS gradient for convergence 0 01 Heating time is 5 00 Sinutation tme psy 5 00 Tine steps between data coltectians 10 Update long range forces every 10 steps Long range force cutoff gt 10 000 A Start Write Job Files Figure 7 4 The Parameters folder of the Liaison panel Simulation temperature This option is available for Hybrid Monte Carlo and Molecular Dynamics sampling It sets the simulation target temperature in Kelvin Temperature relaxation time This option is available for Hybrid Monte Carlo and Molecular Dynamics sampling It sets the time scale in picoseconds on which heat exchanges with the heat bath Residue based cutoff distance This text box sets the value for the cutoff distance All pairwise interactions of an atom in residue i with an atom in residue j are included on the nonbonded pair list if any such pair of atoms is separated by this distance or less The default value is 15 126 FirstDiscovery 3 0 User Manual Chapter 7 Liaison Use ligand input partial charges if they exist Selecting this check box indicates that the partial charges in the input ligand Maestro files should be used instead of charges assigned by the force field atomtyper If you have high quality partial charges from for example ab initio electrostatic potential fitting then this option can
227. t because any given ligand will have nearly identical similarity scores with respect to each of them Including diverse compounds by contrast will help ensure that a ligand that is likely to be a good binder will have high similarity to at least one of them Filename of known inactives Select a file containing the decoy compounds to be used in calibrating similarity weights The file must contain at least one structure Note that these need not be known inactives in the sense of experimental evidence that they do not bind to the target receptor Instead they should be compounds that lack certain features known to be characteristic of the FirstDiscovery 3 0 User Manual 99 Chapter 6 Glide actives or else randomly chosen compounds that probably don t bind or probably are dissimilar to the actives The inactives should be a diverse set of compounds but there are no specific criteria for selecting them The files of active and inactive compounds may be in either Maestro or MDL SD format Percentage of inactives to keep This must be an integer from 1 to 100 Structures from the inactive compounds file are selected at random until the specified percentage approximately is obtained and only the selected structures are used in weight calibration For best results choose the percentage based on the relative size number of structures in the active and inactive files in order to Glide glide Job glidetmp Login dya11 Hos
228. t localhost 1 Settings Site ugana Searing output Constraints Similarity W Generate weights Choose Format Maestro Filename of known actives Choose eS Choose Format Maestro Filename of known inactives Choose es gt Percentage of inactives to keep 10 E Filename of known actives E zi omnee ee g Base penalty vale 6 00 kcalinel Fully penalize liganmis with smilanty 0 30 Ha penalty far Hganis with simitanity 0 70 Reject fuands with sam anty lt 0 00 iiganis with shnilarities between 0 38 ant 0 70 wil be partially penalized Start Write Job Files Hide Help Figure 6 12 The Similarity folder Generate weights 100 FirstDiscovery 3 0 User Manual Chapter 6 Glide obtain a total number of inactives between 5 and 15 times the number of actives Weight calibration may produce a message stating that it did not converge more likely the higher the ratio of inactives to actives but this is not a problem A valid weights file is produced in any case and contains the best weights obtained with the given structures 6 9 3 Similarity Folder Features Docking When the Glide task Dock one or more ligands is selected in the Settings folder the Use similarity score in docking option becomes available in the Similarity folder Use similarity score in docking Selecting this option makes the following features available Filename of
229. tarting the fitting calculation make sure that you are in the Maestro working directory and enter the name of the Master Liaison Run Directory in the Job text box in the upper left corner of the Liaison panel 7 3 2 Predicting Binding Affinities of New Ligands To run a Liaison prediction calculation the following items are required Values for the coefficients of the selected binding energy model equation usually taken from a Liaison fitting calculation A list of ligand names either contained in a file or entered as a comma or space sep arated list in Maestro If the ligand names are in a file you can separate them by one or more spaces a comma or a Carriage return 7 4 The Liaison Panel To run a multiple ligand job or to fit calculated Liaison results to known binding energies you must supply an external file Multiple ligand jobs require an input file listing the ligands to be used and the loca tions of the associated structure files Fitting Liaison results requires a file that lists the ligands and their binding energies When you submit a Liaison job or click the Write Job Files button Maestro writes several files and directories to disk in the Maestro working directory the directory Maestro is in when the job is started or job files are written Specifically it uses the name entered in the Job text box of the Liaison panel to create a Master Liaison Run Directory under the launch directory if the directory
230. te entry from workspace Create an entry in the current project using the contents of the Workspace Show Hide Build panel Show the Build panel or hide it if it is displayed Local transformation Pick the object to transform Menu but ton with a pick menu and an item to open the Advanced Transformations panel Fit to screen Scale what is displayed to fit into the Workspace and reset the center of rota tion Set fog display state Menu button Automatic means on when there are more than 40 atoms in the Workspace off when there are fewer Rotate around X axis by 90 degrees FirstDiscovery 3 0 User Manual r1 ERE Bs ya Q X Import structures Show the Import panel Save as Open the Save Project As dialog box to save the project with a new name Delete Choose an object to delete Menu button with a pick menu a section to delete hydrogens and waters and to open the Atom Selection dialog box and a sec tion to delete other objects associated with the structures in the Workspace Add hydrogens Pick atoms for hydrogen treatment Menu button with a pick menu and an item to open the Atom Selection dialog box Undo Redo Undo or redo the last action Performs the same function as the Undo item on the Edit menu and changes to an arrow pointing in the opposite direction when an Undo has been performed indicating that its next action is Redo Clear workspace Clear all atoms from the Works
231. tes of the training set ligands and its Analysis task is used to derive values for the a D and y fitting coefficients The fitted equation can then be used to predict the binding affinities of additional ligands FirstDiscovery 3 0 User Manual 113 Chapter 7 Liaison Liaison also calculates the GlideScore over the course of the LRM simulation The average GlideScore can then be used to predict binding energies using the alternate model AG a lt GlideScore gt b where a is the GlideScore coefficient Slope and b is a constant Intercept The GlideScore alternative binding energy model can be selected in the Liaison panel s Analysis folder The analysis task will then derive values for the a and b fitting coeffi cients The GlideScore binding energy model is discussed further in Section 7 3 on page 118 and Section 7 9 on page 132 7 2 Liaison Simulations When you start a Liaison simulation from the Maestro interface or when writing job files for a manual submission several actions occur in the background This section describes some of these background features 7 2 Liaison Directory Structure Figure 7 1 on page 115 shows a schematic overview of the Liaison directory structure where Maestro Working Directory is the directory in which Maestro is running when you start a Liaison job or elect to Write Job Files Files in brackets are created only with Liaison Dynamics and HMC jobs Note When you run a Liaison job r
232. the Begin Undo Block command was issued 2 10 Running and Monitoring Jobs While FirstDiscovery jobs can be run from the command line we suggest that you use the Maestro GUI to set up and launch these jobs at least until you have some experience with the programs and understand the directory structure and the input file requirements Maestro has dedicated panels for each product for preparing and submitting jobs To use these panels make the appropriate choice for the product and task from the Applications menu and its submenus 24 FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Monitor monitor Dex Monitoring job grids H01 amp IMPACT I openwt Request to open FORMATTED file grids H01 out on unit 2 Host Linux nahid schrodinger com 2 4 18 24 7 x 1 Fri Tan 31 07 06 03 EST 2003 i686 JobId nahid 0 40b 8c d SCHRODINGER directory software archive 2004 1 pb2 IMPACT EXEC directory software archive 2004 1 pb2 impact v30508 bin Linux x86 MMSHARE EXEC directory software archive 2004 1 pb2 mnshare v13005 bin Linux x 86 amp IMPACT I foldmain calling opls2001 atomtyping amp IMPACT I foldmain finished parameter assignment VdW radii of protein atoms scaled by 1 000000000000000 Charge cutoff for polarity 0 2500000000000000 XIMPACT I xdrwt File home saunders Documentation FirstDiscovery Tutorial tutorial grids grids CALCSITES calling blduserlig for CM range Monitor Detach
233. the enclosing box to 50 74 FirstDiscovery 3 0 User Manual Chapter 6 Glide 6 4 1 Site Folder Features The Site folder defines parameters for calculating grids The options in this folder are described below Specify center of enclosing box by These buttons determine how the scoring grids are centered There are three options The Ligand centroid option centers the grid box at the centroid of the ligand dis played in the Workspace This is the default option when a ligand has been identified and marked in the Workspace When you have selected this option the Specify Glide glide Job grids_H01 Login saunders Host localhost 1 settings Site ugana Searing output constraints simitarity Specify center of enclosing box by Ligand centroid Specify Ligand ww Active site residues Supplied X Y Z coordinates X 2 1893 2 1411 amp 2 6517 Size of bounding box for placing ligand center 10 A Y v Size of enclosing box Fit displayed ligand ww Fit ligands with length lt 20 00 Scaling of vdW radii for nonpolar receptor atoms Scale radius if partial atomic charge lt 0 25 Scale by 1 00 W Display bounding box for ligand center green W Display enclosing box purple Start Write Job Files Hide Help Figure 6 4 The Site folder of the Glide panel FirstDiscovery 3 0 User Manual 75 Chapter 6 Glide
234. the file containing the active compounds need not be specified until the ligand docking job Weighted Similarity Scoring as the name implies counts some AP matches more than others This scoring method requires specification of a set of decoy compounds often referred to as inactives but not necessarily known experimentally to be inactive in addi tion to the actives and uses both sets during a grid generation job to calculate a set of cali brated weights for the atom pairs found in the active compounds Specifically APs found only in active compounds receive higher weights than those found in both actives and inactives In a subsequent docking job when Glide computes the similarity score of a given ligand to be docked it applies these weights to the atom pairs found in that ligand An AP found in a ligand that was not encountered during weight calibration i e did not occur in either the actives or the inactives is assigned an average weight of 1 0 by default Weighted similarity scores may help identify ligands that share specific character istics with the actives that are absent from the inactives i e a common pharmacophore For either method of similarity scoring the Glide docking job adjusts the GlideScore of each ligand based on the highest similarity of that ligand to any active compound If the 98 FirstDiscovery 3 0 User Manual Chapter 6 Glide highest similarity is s the adjustment is a penalty function f s
235. the input files However this is not recommended When setting up Liaison jobs from Maestro delt and nmdmc remain constant while mxcyc and nstep are increased decreased to accommodate the user specified simulation time Example Dynamics method Simulation time 5 ps Resultant input file LRM section only sample DYNAMICS input cntl nstep 5000 delt 0 001 relax 0 01 nprnt 100 seed 101 5 0 001 5 000 steps The five fold reduction in the number of HMC steps mxcyc reflects the fact that each composite HMC step includes five MD steps Time steps between data collections This text box sets the number of time steps between data collections of the ensemble aver ages during the Liaison sampling Entering 10 in this box the default value produces a line like the following in the LRM task of the Liaison input file input cntl average every 10 file lia free ave Update long range forces every n steps This option is available only for the Truncated Newton algorithm The default is to update long range forces every 10 steps Between updates estimates of these forces are used Smaller values of n more frequent updates can be used to improve convergence but will make the optimization slower The maximum recommended value is 20 FirstDiscovery 3 0 User Manual 129 Chapter 7 Liaison Long range force cutoff gt n Angstroms This option is available only for the Truncated Newton algorithm and specifies the distance beyo
236. the receptor atom must be a metal ion Metal ligand constraints can also include restrictions on the formal charges of the inter acting ligand atoms These requirements are added during setup of docking jobs The receptor atoms selected must also be close enough to the ligand to make satisfying the constraints feasible You do not need to specify any individual distances or angles between receptor and ligand atoms The appropriate bounding values for these measurements are FirstDiscovery 3 0 User Manual 95 Chapter 6 Glide part of Glide s chemical knowledge Distance requirements are incorporated using the enclosing box for the ligand the region in which ligand atoms may be found When the enclosing box has been defined Maestro displays the box in purple The receptor atoms selected for constraints must be inside this purple enclosing box or within bonding range of it When constraint setup is complete and the grid generation job is run Glide will write a file containing the information about the specified receptor atoms their locations and types Subsequent docking jobs will use this file in order to determine whether a given ligand pose satisfies the constraints If the base name for writing grid files is gridbase then the file will be called gridbase cons Glide docking will get the constraints information it requires from gridbase cons Glide glide Job dock_confgen Login saunders Host localhost 1 Settings S
237. the soaked system The soaked output structure will automatically be loaded into the Project Table if you submitted the job from a Maestro project and monitor the job while or after it completes Alternatively you can import this file into Maestro manually or use it for another purpose To open the Soak panel n the Maestro Applications menu choose Soak from the Impact submenu In the upper part of the panel are the standard FirstDiscovery panel options for Job name Login and Host as well as Source of job input and Incorporate output into project by For a description of these options see Section 1 2 The default job name for Soak jobs is impacttmp The input structure for a Soak job can be either the contents of the Workspace or a single entry in the Project Table To run Soak on a system composed of multiple entries 1 Include only those entries in the Workspace 2 Select Workspace as the Source of job input To model active sites or water shells around proteins with explicit solvent Run Soak 2 Run a short minimization and constant temperature MD equilibration at room tem perature By default Soak places 216 water molecules in the smallest permitted solvent box at least 18 62 in each dimension The resulting box is not equilibrated due to edge effects A short minimization is usually sufficient to obtain a fully equilibrated solvated system It is recommended that constant temperature molecular dynamics descri
238. ting information ner ttes 169 MENU Dultoil terere teet 8 Merge entries si ies 139 metal in active site 69 72 metal ions in receptor sese 95 metal ligand interaction 95 metal ligand score see 90 minimization conjugate gradient eee 163 convergence criteria oo eee eee 164 cycles MAXIMUM eese 163 Truncated Newton 163 164 Minimization folder QSite 143 MM potential energy eene 140 MM region 142 160 Mol2 format teile 81 molecular dynamics MD 165 molecular mechanics electrostatic treatment 154 parameter file wo sss 154 Monitor panel eee 25 mouse functions see 5 Project Table panel 16 17 Workspace itte ere Ti MONE sen eoe etre oie 42 43 multimeric protein structure 38 multiple processors 33 148 Glide isi seite teint 110 T Aa1S0n eese c eins 121 136 N neighbor list frequency updating 157 neutralizer brief description 61 nitrogen centers trigonal 83 nonbonded interaction energy 87 nonpolar atoms O onlime help eee 26 179 OPLS1999 OPLS2000 OPLS2001 FirstDiscovery 3 0 User Manual
239. ting structures and configuring the Project Table Select menu provides commands and access to the Entry Selection dialog box and the Filter panel so that you can select entries Entry menu provides tools for including and excluding entries controlling the display of entries in the Project Table and performing various operations on the selected entries Property menu provides tools for displaying and manipulating properties ePlayer menu provides access to the play controls and the ePlayer options 2 4 3 Selecting Entries Many operations in Maestro are performed on the entries that are selected in the Project Table The Project Table functions much like any other table you select rows by clicking shift clicking and control clicking However because clicking in an editable cell of a selected row enters edit mode you should click in the Row column to select entries See Section 2 4 5 on page 16 for more information on mouse actions There are shortcuts for selecting classes of entries on the Select menu In addition to selecting entries manually you can select entries that meet a combination of conditions on their properties Such combinations of conditions are called filters Filters are Entry Selection Language ESL expressions and are evaluated at the time they are applied For example if you want to set up a Glide job that uses ligands with a low molec ular weight say less than 300 and that has certain QikP
240. tion or dynamics Clicking the Frozen Atoms button opens the Frozen Atoms panel which selects the atoms to be treated as frozen The Frozen Atoms panel is described on page 161 Buffered Atoms This button opens the Buffered Atoms panel Use this panel to select the atoms to be treated as buffered Buffered atoms are allowed to move subject to harmonic penalty function restraints that tether them to their initial positions The Buffered Atoms panel is described on page 162 9 5 2 The Frozen Atoms Panel Use the Frozen Atoms panel to specify a set of atoms to be frozen during an Impact mini mization calculation or dynamics simulation Open the Frozen Atoms panel by clicking the Frozen Atoms button in the Impact Constraints folder To define frozen atoms use the Pick options the All button or the Atom Selection dialog box click the blue Select button Selected atoms are listed at the top of the Frozen Atoms FirstDiscovery 3 0 User Manual 161 Chapter 9 Energy Minimization panel If Show Markers is selected the atoms to be frozen are marked with a red padlock in the Workspace These markers can be hidden by deselecting Show Markers in the ASD The Delete button at the bottom of the panel removes the currently selected frozen atom from the list The Delete All button removes all currently defined frozen atoms from the list Note These frozen atom selections are keyed to the Workspace structure that you see on screen If you c
241. to the Workspace structure that you see on screen If you choose Selected entry instead of Workspace as the Source of job input your buffered atom set is not used 9 6 The Minimization Folder The basic settings of the Impact energy minimization task are defined in the Minimization folder 162 FirstDiscovery 3 0 User Manual Chapter 9 Energy Minimization Impact Energy Minimization imini Job impacttmp Login saunders Host localhost 1 Source of job input 4 Workspace gt Selected entry Incorporate output into project by Appending new entries Replacing existing entries lt gt Do not incorporate Potential Constraints Minimization Maximum minimization cycles 100 Algorithm Truncated Newton initial step size 0 05 Maximum step size 1 000 Convergence criteria Energy and gradient Energy change criteria 0 1 Gradient criteria 0 2 Update long range forces every 10 steps Long range force cutoff gt 10 000 A Start Write Job Files Hide Help Figure 9 3 The Minimization folder of the Impact Energy Minimization panel Maximum minimization cycles This text box sets the maximum number of cycles for the minimization calculation The minimization terminates if it has not converged by this point The default value is 100 iter ations but you can specify any value greater than or equal to zero Zero cycles is a special case it instructs Impact just to evaluate the
242. toms Menu button with a list of predefined atom cat egories and an item to open the Atom Selection dialog box Undisplay Undisplay the selected atoms Menu button with a list of predefined atom cat e E 4 egories and an item to open the Atom Selection dialog box Show hide or color ribbons Menu button with items to control the display of ribbons and atoms for pro teins and to color ribbons by various schemes Draw atoms in CPK Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Draw bonds in tube Pick atoms for representation Menu button with a pick menu and an item to open the Atom Selection dialog box Color residue by constant color Pick residues to apply the selected color Double click to color all atoms Menu button with a list of colors Label picked atoms Menu button with a pick menu and items to open the Atom Selection dialog box to open the Atom Labels panel at the Composition folder and to delete labels FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro Display H bonds a Measure distances angles or dihe Pick molecules to display H bonds H drals Menu button with items to choose to 4 Pick atoms to define measurements display H bonds within the selected Menu button with items to choose molecule intra or between the selected between distance default angle or molecule and all other atoms in the d
243. tor n Ask for monitoring files to be sent every n sec cancel Cancel a job that has been launched but not started purge Remove completed job from the database The job selection argument consists of one or more JobIds job names status codes or queries This field is optional if job selection is omitted the default selection is the query status completed that is all active jobs It can also be the word a11 to select all jobs in the jobs database For the complete list of job control actions use the help option to print a usage summary which also provides a summary of query construction with examples For more on the job control facility see the Maestro User Manual For the purpose of killing Liaison jobs the 1ist or show actions can be used to list the jobs in the jobs database and ki11 jobname or ki11 jobid can then be used to kill one of these jobs The top level simulation script is called simulate jobname This script launches a job named jobname sim Use the JobId corresponding to this job as the argu ment to jobcontrol kill jobid all the individual ligand sub jobs are killed as well The job name jobname sim can be substituted for the JobId in the kil1 command FirstDiscovery 3 0 User Manual 137 Chapter 7 Liaison 138 FirstDiscovery 3 0 User Manual Chapter 8 QSite 8 1 Using QSite QSite performs quantum mechanical molecular mechanical QM MM calculations using Jaguar for the OM calculations a
244. tory structure and job files by hand or with an automated script The assumption is that you have used Maestro to create the necessary directory structure and to write the required job files If you want to automate the process use Maestro written scripts as templates To run a Liaison simulation from a terminal window change to the Maestro working directory and enter the following command at the shell prompt simulate jobname This command runs the simulate jobname script that Maestro writes to the Maestro working directory Several relevant lines from such a script are shown below The script shows that the job covers 5 ligands Ligl Lig5 Note the use of backquotes JOB NAME liaison JOB LIST echo Ligl Lig2 Lig3 Lig4 Lig5 NPROC 1 You could run a specific ligand from the command line by altering the JOB LIST line in this script or in a copy of it For example to run only the 1bkm 3m 2 ligand the JOB LIST line should appear as JOB LIST echo 1bkm 3m 2 Provided that the requisite directory structure and input files exist additional ligands can be run by adding to the JOB LIST line Liaison simulation jobs which are more computationally intensive than analysis jobs can be run on several processors simultaneously by appropriately setting the variable NPROC either in Maestro or by editing the simulate jobname file For NPROC gt 1 NPROC jobs will run concurrently When one job finishes another one will start
245. ts original state That is modifications are discarded and do not affect the original pose in the pose list Previous This button selects and displays the entry row that directly precedes the first selected entry row Click Previous at the start of the list to take you to the end Next This button selects and displays the entry row that now directly succeeds the last most selected entry row Click Next at the end of the list to return you to the top FirstDiscovery 3 0 User Manual 105 Chapter 6 Glide Visualize H Bonds to Receptor This button displays markers for hydrogen bonds between receptor and non receptor molecules in the Workspace This button is enabled only when the receptor and at least one ligand pose are displayed in the Workspace Clicking this button alters the H bond Set 1 as listed in the H Bonds folder to be the receptor molecule or molecules and the H bond Set 2 to be all other molecules This action also displays the H bond markers The hydrogen bond settings can be viewed and altered in the H Bonds folder which can be opened either from the Glide Pose Viewer Panel or from the Measurements Panel on Maestro s main menu bar Visualize Contacts to Receptor This button displays the bad and ugly really bad contacts between the receptor and non receptor i e ligand molecules in the Workspace This button is enabled only when the receptor and at least one other pose structure are displayed in the Workspac
246. ture files The identity of a user created text file containing the ligand names and structure file loca tions can be entered directly into the Filename text box Alternatively the Browse button adjacent to the text box can be used to activate the Open File panel to aid in locating the file The identity of the selected file is then displayed in the Filename text box The name of the text file cannot be the same as the name of the Master Liaison Run Direc tory the name that is specified in the Job text box If it is Maestro will display an error message The content and structure of the file is illustrated below 1bkm 3m 1 home user structs 1bkm 3m 1 mae 1bkm 3m 2 home user structs 1bkm 3m 2 mae 1bkm 3m 3 home user structs 1bkm 3m 3 mae The first column contains the user defined ligand name and the second gives the directory path and file name of the ligand structure file Liaison uses each ligand name to create a FirstDiscovery 3 0 User Manual 123 Chapter 7 Liaison correspondingly named ligand directory under the Master Liaison Run Directory Only spaces not tabs or commas can separate the ligand name and file location 7 6 2 Single Ligand Single Receptor A single ligand simulation requires a receptor structure and a ligand structure The receptor structure is taken from the Workspace It may be alone in the Workspace or may be accompanied by the ligand to be simulated The selection options for this Job Type are described
247. type Impact offers three choices Constant temperature NVT Constant energy NVE Constant pressure NPT Depending on the ensemble chosen various subsidiary settings become active Constant temperature NVT With this ensemble type volume and temperature are held constant during the simulation This selection results in coupling the system to an external heat bath with a target temper ature that is the same for all molecular species Two settings become available when this ensemble type is chosen Target temperature This text box sets the target temperature for a NVT or NPT simulation The actual temperature will fluctuate about the target value At each MD step the velocities will be scaled so that the temperature will approach the desired value on a timescale determined by the Temperature relaxation time parameter The default temperature is 298 15 K The acceptable range is any value greater than or equal to 0 K Temperature relaxation time This text box sets the temperature relaxation time in picoseconds for velocity scaling The default value is 0 01 ps The acceptable range is any value greater than 0 ps Constant energy NVE With this ensemble no temperature volume or pressure scaling is done Note that with this ensemble type the total energy may not be conserved if cutoffs on nonbonded interac tions are used as will often be the case or if too long an MD time step is used In most cases failure to c
248. ults from previous Impact calculations run from the cor responding jobname inp file An Impact output structure file written in the Maestro file format Glide Liai son and some other Impact jobs do not write out mae output structure files Glide s intermediate structure files 3 3 The Impact Command Usage Summary The options that you can specify when initiating jobs from the command line are described in Table 3 2 and Table 3 3 To view the following usage summary information define the SCHROI in a command she Syntax DINGER environment variable and enter SCHRODINGER impact h ll impact options i input file FirstDiscovery 3 0 User Manual 29 Chapter 3 FirstDiscovery from the Command Line Table 3 2 Impact Command Options Option Description h Prints usage summary and exits v Prints version number of startup script and exits i input file Impact input file conventionally ending in inp If the input file argu o output file s size Liaison Only Options liasim d dir c controlfile 1 datafile n jobname x outfile QSite Only Options j jaguar file p num proc ment does not end in inp Impact looks first for input file as specified If that doesn t exist it then looks for input file inp The switch for this argument i is optional but if i is omitted then input file must end in inp and must be the last argument in the com mand line Fi
249. umber of component terms retained in the reciprocal space part of the Ewald summation The default value is 5 Larger values yield increased accuracy but result in slower execution Alpha This text box sets the value of the parameter alpha in the Ewald method A reason able value 1s 5 5 L where L 1s the linear dimension of the cubic simulation box The default value is 0 25 9 4 6 The Continuum Solvation Panel Impact supports two implicit solvent models the Surface Generalized Born Model SGB and the Poisson Boltzmann Solver PBF These methods simulate the effects of solvent without the use of explicit solvent molecules To open the Continuum Solvation panel select Use continuum solvation and click Settings The selection options of the Continuum Solvation panel are Solvation Method The Solvation Method menu options are Surface Generalized Born Model SGB the default which is unavailable if Use fast multipole method has been selected Poisson Boltzmann Solver PBF which is unavailable if the Truncated Newton min imization algorithm has been selected SGB Displacement Threshold This text box specifies how far any atom may move from the coordinates used in the previous SGB calculation before a new SGB calculation must performed If no atom has moved this distance the previously calculated SGB energy and forces are used PBF Resolution The Poisson Boltzmann solver involves a finite element calculation on
250. until all receptor ligand pair simulations have been submitted Of course you need to have sufficient Liaison licenses to run the requested number of jobs Liaison Fit or Predict jobs can also be started from the shell prompt by running the fit Jjobname or predict jobname script Maestro writes to the Maestro working direc tory However fitting and prediction calculations are virtually instantaneous once the prerequisite simulation calculations have finished and it is usually more convenient to submit such jobs directly from the Maestro interface 136 FirstDiscovery 3 0 User Manual Chapter 7 Liaison 7 11 Killing Liaison Jobs The job control facility may be used to manage and if necessary kill Liaison jobs This facility can be invoked from the Maestro Monitor panel To kill a Liaison job select the jobname_sim entry and click the Kill button and all the subjobs will quit as well Liaison jobs can also be controlled from the command line with the jobcontrol command SCHRODINGER jobcontrol action job selection where action is one of the following and job selection specifies one or more jobs The action will be applied to each selected job list List the JobId job name and status By default lists all active jobs show Show basic information about the job kill Terminate the job immediately stop Terminate the job as soon as possible pause Suspend the job temporarily resume Continue running a paused job moni
251. ure file format Glide supports the three file formats listed below for reading ligand files Glide does not support Mol2 formatted files Note that Glide automatically skips fragmented ligands e g salts with counterions present ligands containing lone pairs and ligands containing unparameterized elements e g arsenic e Maestro Maestro written files extensions mae out or dat One file may be specified e MDL SD SD formatted files extensions mo1 for single structure files and sdf for multiple structure files One file may be specified FirstDiscovery 3 0 User Manual 81 Chapter 6 Glide PDB Rutgers Center for Structural Biology Protein Data Bank files extensions pdb or ent When this option is chosen more than one file can be specified Specify one or more file s in format format This list specifies the ligand files Glide will dock listed in order of user entry when PDB format is used The file formats given in the Ligand structure file format option menu are supported To add a file click Add File The Add ligand structure files panel is displayed In this panel ligand files can be selected and opened for placement in the list The two buttons to the right of the Add File button allow you to remove files already placed in the list The Remove File button removes a highlighted ligand file and the Remove All button removes all listed ligand files For PDB format any number of ligand files may be
252. ures Open the Import panel for importing structures into the project Export structures Open the Export panel for exporting structures to a file Columns menu Display a menu for adjusting the column widths Entry selection Open the Entry Selection dialog box for selecting entries based on criteria for entry properties Go to start Display the first selected structure Previous Display the previous structure in the list of selected structures Play backward Display the selected structures in sequence moving toward the first Stop Stop the ePlayer Play forward Display the selected structures in sequence moving toward the last Next Display the next structure in the list of selected structures Go to end Display the last selected structure ePlayer loop menu Display a menu of options for repeating the display of the structures Single direction displays structures in a single direction then repeats Oscillate reverses direction each time the beginning or end of the list is reached FirstDiscovery 3 0 User Manual Chapter 2 Introduction to Maestro The status display shows the number of selected entries When you pause the cursor over the display the Balloon help shows the total number of entries the number shown in the table the number selected and the number included 2 4 2 The Project Table Menus Table menu provides tools for finding text sorting entries and plotting properties importing and expor
253. very 3 0 User Manual Chapter 4 Protein Preparation 4 10 2 Resolving H Bonding Conflicts One or more residues may need to be modified to resolve an acceptor acceptor or donor donor clash If residues need to be modified follow these steps 1 Place the refined protein ligand complex in the Workspace 2 Examine the interaction between the ligand and the protein and or the cofactor 3 Use your judgment and chemical intuition to determine which protonation state and tautomeric form the residues in question should have 4 Use the structure editing capabilities in Maestro to resolve the conflict Some of these clashes are recognized by the preparation process but cannot be resolved by it The preparation process may have no control over other clashes An example of the latter typically occurs in an aspartyl protease such as HIV where both active site aspar tates are close to one or more atoms of a properly docked ligand Because these contact distances fall within any reasonable cavity radius the carboxylates are not subject to being neutralized and will both be represented as negatively charged by the preparation process However when the ligand interacts with the aspartates via a hydroxyl group or similar neutral functionality one of the aspartates is typically modeled as neutral 4 11 Command Line Protein Preparation To run protein preparation from the command line 1 If you do not yet have receptor and ligand structure files
254. x click the Select button You can select an atom group from any of the folders in the dialog Atom Selection Select To Delete atom Resiaue Molecuie cnain entry smsna ser Sequence Residue Type Residue Mu Add Backbone Side Chain Subtract Secondary Structure Intersect Atoms Matching 96 ASL W Show markers res num gt 200 j Proximity 7 Create Set All Undo Sec Clear Invert Matching 800 atoms OK Cancel Help Figure 2 4 The Atom Selection dialog box FirstDiscovery 3 0 User Manual 21 Chapter 2 Introduction to Maestro box Atom Residue Molecule Chain Entry Substruct Notation or Set You can then combine this group with the existing atom group using the buttons on the right the Add button Boolean OR includes all atoms in the new group or the existing group the Subtract button Boolean AND NOT excludes atoms in the new group from the existing group and the Intersect button Boolean AND includes only those atoms that are in both the new group and the existing group The existing group is expressed in Atom Specifica tion Language ASL in the ASL text box and is shown with light blue markers in the Workspace The current selection is shown with purple markers When you are satisfied with the selection click OK to apply the operation you have chosen to the selection you have made The operation is described in a bar at the top of the Atom Selection dialog box
255. x specifies the base name basename for the grid files This name is used to find the grid files when existing files are being used for the calculation or to name the grid files when the grids are being calculated and saved By default the base name of the grid files is set to the job name in the Job text box The default job name is glidetmp Directory for grid files This text box specifies a directory that the grid files are to be read from or written to By default this is set to the current working directory FirstDiscovery 3 0 User Manual 73 Chapter 6 Glide 6 4 The Site Folder The Glide Site folder determines where the scoring grids are positioned throughout the receptor and how they are prepared from the structure in the Workspace The Site folder is enabled only when Choose Glide function in the Settings folder is set to Set up grids This folder is not used in preparing Dock one or more ligands jobs Glide uses two boxes to organize the calculation The grids themselves are calculated within the space defined by the purple enclosing box This is also the box within which all the ligand atoms must be contained Acceptable positions for the ligand center must lie within the green bounding box This box gives a truer measure of the effective size of the search space The only requirement on the enclosing box is that it be big enough to contain all ligand atoms when the ligand center is placed at an edge or vertex of the b
256. yal Host localhost 1 Source of job input 4 Workspace Q Selected entry Incorporate output into project by Appending new entries Replacing existing entries Do not incorporate Potential constraints Minimization Optimization QM Settings Minimization options for the MM region Maximum minimization cycles 100 Algorithm Conjugate gradient Initial step size 0 05 Maximum step size 1 000 Convergence criteria Energy and gradient Energy change criteria 0 1 Gradient criteria 0 2 Start Write Job Files Hide Help Figure 8 3 The Minimization folder of the QSite panel 8 6 The Optimization Folder The QSite Optimization folder specifies the QM Jaguar calculation to be performed and identifies any additional structures that may be needed Single point energy calculation no geometry optimization Geometry optimization to a minimum energy structure Geometry optimization to a transition state TS using one of three methods e Standard Linear Synchronous Transit LST e Quadratic Synchronous Transit QST Note QSite QM geometry optimizations use Cartesian coordinates only Transition state optimization by the Linear Synchronous Transit method requires initial guess structures for the reactant and the product The Quadratic Synchronous Transit method requires initial guesses for the reactant product and transition state structures 144 FirstDiscove
257. ydrogen bond or metal ligand interactions that you think are important to the binding mode By setting such prerequisites often you can significantly enrich the final results and speed up docking as Glide is able to discard ligands conformations or poses that do not meet these criteria early on in their evaluation for docking suitability 6 8 1 Using Glide Constraints To use Glide constraints you must perform both of these steps 1 Define Glide constraints during grid generation setup 2 Apply Glide constraints during docking setup Any Glide constraints you would like to apply to docking must be defined when the receptor grids are generated When you are specifying options for the Set up grids job open the Glide Constraints folder and select atoms in the receptor which you would like to interact with the ligand during docking It may be helpful to undisplay most of the receptor leaving only residues within a short distance of the ligand visible As it is picked each receptor atom is marked with a red cross and padlock in the Work space Receptor atoms that are symmetry equivalent to the one picked are part of the same constraint and are marked along with the picked atom You can define up to ten different Glide constraints for a single grid generation job As well as being marked in the Work space they are listed in the Glide Constraints folder Receptor constraint sites box Symmetry equivalent atoms appear in square brackets Wh
258. ype and number and chain separated by colons Symmetry equivalent atoms defined by a single constraint are separated by commas within square brackets Select highlight the constraints to be used in docking If none of the constraints in the list are selected the docking job will proceed without using Glide constraints Ligand atoms interacting with receptor metal sites For a docking job with Glide constraints involving metal binding interactions you must provide one more piece of information You need to choose whether ligand atoms will be required to have a specified formal charge in order to be considered as satisfying constraints The choices are Must be charged the default and usually the best choice Must be neutral or May be either charged or neutral Glide will apply the requirement you choose for binding to all receptor metal ions you have selected for constraints Note that for a ligand coordinating group such as a carboxylate the two oxygens are regarded as having non zero formal charges of 0 5 Therefore either oxygen can be used to satisfy the constraint provided that Must be charged or May be charged or neutral is selected FirstDiscovery 3 0 User Manual 97 Chapter 6 Glide 6 9 The Similarity Folder 6 9 1 Introduction to Similarity Scoring in Glide Similarity scoring is a means of quantifying how much alike or different two molecules are In Glide similarity scoring enables you to reward or penalize ligands based o

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