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Desmond Tutorial - DE Shaw Research

1. Select Undo Redo Delete Sketcher AddH Transform Adjust ES X X X Find Atom number l N P O of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 37656 147743 Entries 1 3_Res 32760 Chn 3 Mol 31968 Chg 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu D E Shaw Research Jobs 0 0 Importing Membrane Placement from the OPM Database 45 Desmond Tutorial Preparing a Desmond simulation with the System Builder This page left intentionally blank 46 D E Shaw Research April 2011 3 Finishing Preparations for Desmond Simulation April 2011 Overview There are a few more tasks that must take place before a simulation can be run e The System Builder will always generate the latest OPLS AA force field parameters for the simulation system it builds and the parameters will be included in the cms output file However you may want to assign different force field parameters in case the Schr dinger provided OPLS AA parameters are not adequate for a particular sys tem You can assign alternative force field parameters for your system using a com panion program to Desmond called Viparr e You will also have to specify Desmond run time simulation parameters These topics are addressed in the following sections along with instructions for importing
2. System Builder automatically assigns the latest OPLS AA force field parameters available in the Schr dinger Suite to the entire system If you would rather apply a Desmond pro vided force field Amber or Charmm force fields TIP5P water model Schr dinger s PFF polarizable force field etc you need to process the cms file using the external Viparr pro gram see Generating Force Field Parameters with Viparr on page 47 You can also generate the solvated system from the command line You may decide to use this method if you want to manually edit the input file to produce an effect that cannot directly be generated by the System Builder To generate the solvated system from the command line 1 Click Write in the System Builder panel to write the job files to disk There are two input files my_setup mae The Maestro structure file of the solute which serves as the input for system setup my_setup csb The command file which can be hand edited for custom setup cases For detailed documentation of the csb file see the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 And a single output file besides a log file my_setup out cms The Maestro structure file of the entire simulation system including OPLS AA force field parameters For details on the cms file see the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 2 Execute the following
3. 000 cee 55 OVETVIE Wied Sos eyes ed Be Gee Sete oh ee ho a ete ee ewe Glo he ees ee 55 Running Simulations from the Molecular Dynamics Panel 55 Running Simulations from the Command Line 0000 56 Running MultiSim jobs from the Command Line 05 58 5 Preparing Free Energy Perturbation and Metadynamics 61 OverVidWr 4 os sea cave deb Eden ow kde ee en we ees he eee et 61 Setting Up an FEP Calculation 2 2 2 ee ee 63 Using Maestro To Generate A Desmond FEP Configuration File 68 Running FEP Simulations from the Command Line 0 70 Creating a Custom Fragment Group 2 2 eee 71 Adjusting the Conformation of the Mutant 000 77 Other Types of Mutations aaa aaa ee 81 Aside Metadynamics noaa aa a 82 6 Visualization and Analysis using Maestro nanaaaaaanananannnnn 87 VERVIEW ie s s fuente E Mac S gts tee For Bea dnd aoa dati e Beak nat 26 87 Animating Desmond Trajectories with the Trajectory Playr avses amp dub wares i dh ee ee eed Ete eas eat 87 Performing Simulation Quality Analysis 2 0 0 0 0 00 00 0000 90 Performing Simulation Event Analysis 2 0 00 00 ee ee ee eee 92 7 System Setup and Trajectory Analysis Using VMD 00000eeeenee 95 OVerview si 26 wees Pie amp we Os EM RAR Meee She haw hl eo e eee os 95 The VMD Python Interface aa en 95 Loading and Viewing Trajecto
4. protonated 2 morpholinoethyl I 3 morpholinopropyl protonated 3 morpholinopropyl 4 morpholinobutyl l protonated 4 morpholinobutyl I 5 morpholinopentyl protonated 5 morpholinopentyl I protonated piperidin4 yl protonated piperidin4 ylmethyl I protonated 2 piperidin4 yljethyl protonated 3 piperidin 4 yl propyl I protonated 4 piperidin 4 y buty protonated 5 piperidin 4 yl penty 2 aminoethylamino 2 ammonioethylamino 2 aminoethylammonio ir Grow Direction Joining Geometry 2 dimethylamino ethylamino a 1 April 2011 D E Shaw Research 75 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 12 Selecting the grow bond r v Maestro 5 E g y 9 Sce o oo 9 3 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color x x y X X X X zke off res pz E Ra pe G G b SN GF D Draw Set Element Bond Order Bond Order Formal Chg Formal Chg Move R S Cleanup Sculpt Find Atom number bd J P 0 of Fit Se Project Edit Use the cursor to select the grow bond in the workspace Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 4 Select propyl from the fragment list in the Fragments tab of the Build panel as shown in Figure 5 11 on p
5. In general there are two alternatives for fixing this type of problem From the H bond Assignment subpanel when you click the Refine tab Click Optimize to launch a comprehensive Monte Carlo search different protona tion states of ASN GLN and HIS residues are sampled and OH bonds are flipped to optimize hydrogen bond geometry As part of this procedure you can switch to exhaustive search mode as well as decide whether the orientation of crystal water molecules should be sampled Click Interactive Optimizer to launch an interactive tool for hydrogen bond geome try optimization The interactive optimizer panel is shown in Figure 1 9 When you click Analyze Network the Protein Preparation Wizard fills in the table with the current protonation states of ASP GLU and HIS residues as well as initial OH bond orientations The table shown in Figure 1 9 reflects the current state after click ing Optimize in the Interactive H bond Optimizer D E Shaw Research 9 Desmond Tutorial Desmond Tutorial Figure 1 9 Protein Preparation Wizard Interactive H bond optimizer NUEG Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window E F D A HE 2 PDB wa Job prefix prepwizard La a 223 a a E bg y S ea Q Q Display hydrogens ONone Polar only OAIl vE Open Save As Import Export Table 2DViewer Lig int GetPDB PrepWiz Fit Fog Enhance Ro R x P Import and Process Review and M
6. Atom number X NPO of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments The attachment bond you selected is shown as a green arrow in the workspace Jobs 0 0 Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 j middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 2 Select the methyl fragment on the Define Perturbation tab and select the View option as shown in Figure 5 9 The view in the workspace will change to that shown in Figure 5 10 72 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Figure 5 9 Selecting the methyl group as the base for the butyl substitution group April 2011 Select Pick the attachment bond Select the methyl fragment as the base of the butyl substitution group e Define Perturbation Plan Calculation Step 1 Display the ligand and its receptor if any in the Workspace Step 2 Pick the attachment bond to define the core and the ep 2 substitution group Step 3 Select fragments that will replace the substitution group Fragment library 9 items 1 item selected Fragment name View Reset 1 methyl Reset 2jethyl e Reset 3 hydroxy C Reset 4 amino O Reset 5 ammonio Q _ Reset 6 carboxy o Rese
7. Glide Impact laquar D E Shaw Research Iv Maestro 4pti prj Applications Workflows Scripts Window Help 2 G ss em Q A F oe Fit Fog Enhance Rotate X Rotate Y Tig d u System Builder Minimization Simulated Annealing Molecular Dynamics Replica Exchanae The System Builder panel appears as shown in Figure 2 2 21 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 2 System Builder panel 22 RA sy stem Builder 27777777A Solvation lons Set Up Membrane Delete Membrane Solvent model None Predefined SPC ih Custom Browse Boundary conditions Box shape Orthorhombic X Box size calculation method Buffer O Absolute size Distances a 10 0 b 10 0 c 10 0 Angles a 90 0 B 90 0 y 90 Box volume 3 Calculate Minimize Volume Show boundary box J Use custom charges Force field OPLS2005 Start Write Reset Close Help J The solvated system generated by System Builder includes the solute protein protein complex protein ligand complex or similar systems or a protein immersed in a mem brane bilayer solvent and counter ions All structural topological information and force field parameters for the solvated system are written to a special Maestro file that is subsequently used for Desmond simulation Selecting Solutes and Solvents The System Builder considers
8. 38 12 J Maestro 4pti prj a g a amp amp Open Save As Import Export Table R RA OA X K Select Undo Redo Delete Sketcher ey E A Scoe Q o Ribbon Wire CPK Ball amp Stick Tube grr P 4 s 219 Project Edit view workspace Style Find Residue number Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help ss PDB 7 Ba aje E ba Yy ea Q A S ale 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile 2 Lal ah H P MS h a 9 Add H Transform Adjust Create Entry Clear Save Image New Scene X a P Thin Tube Color Scheme Color X 7 N P 0 of 0 Fit Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 27359 146065 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu A Note the large J hole within which the protein was inserted Entries 1 14 Res 35622 Chn 3 Mol 34648 Chg 0 Jobs 0 0 More experienced users may want to run the System Builder job from the command line Instead of clicking Start click Write to write a command script file to disk that can be executed from the command line a Click Write in the System Builder panel to write the job files to disk There are two input files my_setup mae This is the Maestro structure file of the solute 1su4 protein cal cium ions crystal water mo
9. ASL syntax or the Atom Selection dialog box The Molecular Dynamics panel is filled in automatically with default parameter values To set your own default values so they are automatically presented in the Molecular Dynam ics panel set the desired values in any of the tabs and save it by clicking Write Then copy the resulting cfg file to schrodinger desmond30 desmond_default cfg The new default values take effect the next time you open the Molecular Dynamics panel Detailed documentation of the Molecular Dynamics run time parameter settings can be found in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 Once you have set values for relevant parameters you are ready to execute a simulation Editing the Desmond Conguration File Directly The Desmond conguration file syntax is described in detail in the Desmond User s Guide see Documentation Resources on page 111 You can edit the Desmond configuration file directly It can be useful to edit existing configuration files that were used in other projects You can always write out a configuration file and use it as a template by click ing Write in the Molecular Dynamics panel D E Shaw Research April 2011 4 Running Desmond Simulations April 2011 NOTE Overview You can run a Desmond simulation from the Molecular Dynamics panel or the command line Before running a simulation you should select Relax the model system before si
10. Adjust Create Entry Clear Save Image New Scene View ene g e oe 2 Q gt D Dd Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color y v y x X X a Y Find Atom number N ejo of I Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments This side chain will be mutated to replace the NH3 with a methyl group Atoms 0 0 14026 Entries 1 6 Res 4425 Chn 2 Mol 4396 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu As shown in Figure 5 1 contact residues in the active site are displayed with a matching molecular surface to emphasize the 3D layout of the active site One of the two NH CH CH NH side chains is colored darker see at the center of the workspace in Figure 5 1 this is the side chain where the terminal NH3 group will be mutated to a methyl by FEP Note that the setup in Figure 5 1 is only an illustration showing a common real life example for FEP calculations however you will not need to perform any docking calcu lations for this tutorial exercise Instead just build the ligand structure using the 2D sketcher tool un check convert to 3D and then click Clean up geometry as shown in Figure 5 2 62 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Setting Up an
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12. OPLS2005 Start Write Reset Close Help j 7 In this tutorial exercise we do not want to place counterions in the vicinity of the cal cium ions This can be achieved the following way Click Select in the Excluded region section The Atom Selection panel opens as shown in Figure 2 8 Figure 2 8 Selecting the excluded region Define transmembrane atoms Atom Residue Molecule Chain Entry Substructure Set Lence Residue type Add P P Residue number Subtract Click the Residue Sa Saeed Classification Intersect tab select Residue ckbone side chain Update Markers Re shots io type and select the Atoms matching CA ions 2 j ASL X Show markers fillres within 5 res ptype CA Click Proximity and Proximity set the distance Create Set All Undo Redo Clear Invert Previous Selection Atom Num Res Num Matching 237 atoms 0K Cancel Help 8 Select the two calcium ions by residue type and click Proximity to select all residues within 5 A The resulting ASL expression at the bottom of the selection panel defines the excluded region Click OK NOTE The Excluded region section in the lons tab in Figure 2 7 also has an option to define a region around the selected atoms but the command in the ASL section fillres within
13. Restraints R Output Misc RESPA integrator Time step fs bonded 2 o near 2 00 S far 6 00 S Cancel Apply OK Help The Advanced Options dialog box has several tabs e Ensemble Contains thermostat and barostat parameters e Interaction Contains parameters for computing non bonded interactions e Restraint Provides a table in which multiple sets of atoms can be subjected to har monic restraint with a user defined force constant Atom selection can be directly input as an ASL expression or you can click Select to bring up the Atom Selection dialog box e Output Includes the names of various Desmond output files and allows you to spec ify how often these files are updated during the simulation For example different energy terms are recorded in the energy sequence file in user defined intervals Snap shots of the simulation are periodically saved in the trajectory file and the entire simu April 2011 D E Shaw Research 53 Desmond Tutorial 54 NOTE NOTE Finishing Preparations for Desmond Simulation lation state is also saved at user defined intervals in a checkpoint file Desmond simulations can be restarted from checkpoint files with bitwise accuracy The Output tab has a very useful option If Glue close solute molecules together is set the Desmond trajectory file will be constructed in such a way that receptor ligand com plexes DNA strands or any other multi molec
14. Select Show boundary box and click Calculate The System Builder can also be instructed to minimize the volume of the simulation box by aligning the principal axes of the sol ute along the box vectors or the diagonal This can save computational time if the sol ute is not allowed to rotate in the simulation box After setting all these options the workspace displays the solute and the boundary box as shown in Figure 1 13 D E Shaw Research 13 Desmond Tutorial Desmond Tutorial Figure 1 13 Solute and boundary box in the Maestro workspace SLL lll Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help aa amp a PDB Ba ae a U eam Fe FT Fie S A amp Open Save As Import Export Table 2D Viewer Lig int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile A r ml my X KH OS MS h b Select Undo Redo Delete Sketcher Add Transform Adjust Create Entry Clear Save Image New Scene ene g A Fi eee amp 6 oO gt gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color y v y a 2 x X Y Find Residue number 219 N elo of 0 Drt Project Edit view Workspace Style Saved Views Display Atoms Representation Labels Build Fragments The solute and boundary box is displayed in the workspace Atoms 0 751 1081 Entries 1 4 Res 120 Chn 1 Mol 61 Chg 6 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center
15. loads just the positions A second type dt rv loads positions as well as veloci ties if they are present in the frames When referring to a Desmond trajectory file there is a special file called clickme dtr that should be used clickme dtr resides in the same subdirectory where all the other trajec tory file pieces are written Knowing the file type will be necessary for loading structure and trajectory files from either the command line or the scripting interface Both structure files and trajectory files can be loaded in three different ways with varying degrees of flexibility and ease of use Loading Files from the Command Line If you are comfortable using the shell and the command line loading files into VMD using command line arguments is the easiest way to go The syntax is vmd mae structure cms dtr trajectory_subdir clickme dtr Launching VMD in this fashion will create a new molecule initialize its structure from the cms file create an initial set of coordinates from that same file and finally append all the snapshots from the dtr file to that molecule D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Loading and Viewing Trajectories Multiple structure and trajectory files can be loaded into separate molecules using combi nations of the m and f options The effect of m is to cause anew molecule to be created for each subsequent file The f option causes subsequent files to be loaded
16. right click on atom spot center right click on atom bond and hold menu April 2011 D E Shaw Research 43 Desmond Tutorial Preparing a Desmond simulation with the System Builder As you can see the placement is quite different from that shown in Figure 2 14 and Figure 2 15 Note the different angle between the transmembrane helices the plane of the membrane and the vertical shift between the two membranes 12 Click OK in the Set Up Membrane dialog box 13 Click Start in the System Builder panel to generate the membrane The full system is shown in Figure 2 24 and Figure 2 25 for comparison with Figure 2 16 on page 37 and Figure 2 17 on page 38 It is clear from the comparison of Figure 2 17 and Figure 2 25 that the OPM placement results in a much better quality immersion of the protein in the lipid bilayer with much less void left in the channel Figure 2 24 Full membrane simulation system for 1su4 Note that the visual artifact discussed with respect to Figure 2 16 on page 37 is even more pronounced here The protein seems to extend into the vacuum Nonetheless because of the periodic boundary conditions this is correct Basically it is a periodic image of the protruding part of the protein at the bottom of the simulation box where there is plenty of water that is used in the computation 44 Kg Maestro 7 Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help me
17. 5 res ptype CA shown in Figure 2 8 takes precedence April 2011 D E Shaw Research 29 Desmond Tutorial Preparing a Desmond simulation with the System Builder Click Advanced ion placement in the lon placement section of the lon tab shown in Figure 2 7 to open the dialog box shown in Figure 2 9 Click Candidates A list of all negatively charged residues which lie outside of the excluded region appear in the table as shown in Figure 2 9 Figure 2 9 Placement of the counterions 30 10 v System Builder Advanced lon Placement x Candidates 23 selected 0 remained 123 total Description Use Shift Click to 20 A ASP 951 select the first 23 residues 21 A GLU 340 22 A ASP 815 24 A GLU 183 P ce 4 po n D A 01o Click OK asala aco J SS X cancel EZH Note that the 1su4 structure has a net total charge of 23 after being processed with the Protein Preparation Wizard The candidate residues are listed in the table in no particular order therefore if you select the first 23 residues a good spacial distribu tion of the positive counterions should result Click OK Temporarily turn off the ribbon view so you can see the visual feedback of candidate selection in the workspace The 1su4 structure should appear similar to the work space in Figure 2 10 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builde
18. 5 1 The command line invocation of the Viparr script is SSCHRODINGER run FROM desmond viparr py but it is referred to as viparr py below viparr py help usage viparr py options mae_file maeff_outfile Description Viparr is a force field parameter assignment program f and d are used to specify force fields the order of force fields is important earlier ones take precedence over later ones Simple example viparr py f charmm27 f spc mae_file maeff_outfile More complicated example viparr py d me myfiles myff f charmm27 f spc mae_file maeff_outfile Available built in force fields amber 03 amber94 amber96 amber99 amber99SB amber99SB ILDN charmm22nocmap charmm27 charmm32 charmm36_lipids oplsaa_impact_2001 oplsaa_impact_2005 oplsaa_ions_Jensen_2006 spc spce tip3p tip3p_charmm tip4p tip4p2005 tip4pew tip5p options version show program s version number and exit D E Shaw Research April 2011 Finishing Preparations for Desmond Simulation Generating Force Field Parameters with Viparr April 2011 h help show this help message and exit cCTNUM run Viparr for one CT block only e g for the first use c 1 fFFNAME built in force field name several can be listed each preceded by its own f dFORCEFIELD user provided force field directory several can be listed each preceded by its own d mMERGE_DIR path to user defined force field directory that is to be merged wi
19. ASL text box This option is useful when the solute appears to jump in and out of the primary simulation box due to a visual artifact caused by the periodic boundary conditions This option only affects visualization the actual trajectory is left intact Click Structure to export selected trajectory frames to the Project Table or to an external structure file Center molecules Pick atoms for frame positioning ASL mol num 1 x All Selection Previous Select Pick Atoms v a m Atoms to display in each frame Always display these atoms _____ ASL sec strand OR res sec loop x all Selection Previous Select 5 o JA Display only specified atoms D E Shaw Research _ _ S _ Structure Image Movie E Use the Atoms to display in each frame option to select a part of the system to display based on the ASL expression Click Movie to generate a high quality MPEG movie of the trajectory animation 89 Desmond Tutorial Visualization and Analysis using Maestro Figure 6 3 Workspace view for trajectory visualization Edit View Workspace Tools Applications Workflows Scripts Window Help Maestro Project a iret eS FE PDB S ra g aje a amp he E ON S 12 Q a OE si Fit Fog Enhance Rotate X Rotate Y Tile Open Save As
20. FEP Calculation Figure 5 2 The ZINC 01538934 ligand structure Click Clean up to convert the structure in 3D Maestro Project Edit View Workspace Tools Applications Workflows Scrij s Window Help biomes K rele A gg Click 2D Sketcher to sh draw the ligand structure D Viewer Lig Int GetPDB Prep Wiz Fit Fog nhance Rotate X Rotate Y Tilg KA H oe S dh d Th Select Undo Redo Deletg ketcherfi dd H Transform Adjust Create Entry Clear Sz Jelmage New Scene S N Vd a E a x E Q J Q er P Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color vor x Y X Ad gt pz z NS 5 2 r g le OF amp D gt Draw SetElement Bond Order Bond Order Formal Chg FormalChg Move R S Clean up Jculpt N Find Atom number X NIPO of 0 Fit E Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 j middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu Setting Up an FEP Calculation To setup a Free Energy Perturbation calculation for ligand mutation 1 Select Applications gt Desmond gt Ligand Functional Group Mutation by FEP The Ligand Functional Group Mutation by FEP panel appears as shown in Figure 5 3 April 2011 D E Shaw Research 63 Desmond Tutorial Pr
21. Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz se e P 4 mw OY X KH OS amp d T b Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image New Scene To create this layout of soo o 00 ay gt the Maestro window the Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color following toolbars have Find Residue number 71219 JNIP O of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments been selected Project Edit Workspace Find and Representation H Atoms 0 0 514 Entries 1 1 Res 118 Chn 1 Mol 61 Chg 6 Jobs 0 0 Maestro workspace middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 2 Import a protein structure file into your workspace by choosing Project gt Import Structures The Import dialog box appears as shown in Figure 1 3 Figure 1 3 Import dialog box uinyc kolossva Play Desmond_Tutorial 0 6 gt 4 sS Home Directory Select the PDB file you tome vsrectory want to import Working Direc Click Options oe lt lt Help Import all structures Replace Workspace rt Fit to Workspace following import End Total 1 Include in Workspace First imported structure v X For Desmond files import only first structure Create groups for Files with mult
22. Read Keywords Write Keywords Export Results n Close J Help SEA can perform two basic types of analysis based on the Desmond trajectory energetic analysis and geometric analysis e Energetic analysis is carried out using a Desmond application called vrun vrun applies single point Desmond calculation on each trajectory frame separately In the context of SEA vrun can be used to monitor a wide range of inter group and intra group energetic terms between pre defined atom groups A typical example is the interaction energy between a ligand and the active site residues of an enzyme For details about vrun consult the Desmond User s Guide listed in Documentation Resources on page 111 e Geometric analysis is used to monitor torsion angles distances and so forth throughout the simulation To begin analysis click Browse next to Structure to select the desmond_job out cms file Then determine the analysis to perform and the atoms to which to apply the analysis from the Properties area which has multiple tabs D E Shaw Research April 2011 Visualization and Analysis using Maestro Performing Simulation Event Analysis April 2011 NOTE The tasks you can perform appear in the middle of the Simulation Event Analysis panel Click Analyze to run the analysis When performing energetic analysis vrun is executed and job progress is displayed in the Job Monitor panel After analysis tasks have be
23. Review and Modify Refine Import structure into Workspace fisua O iffracti Biolonical unit P PDB 1su4 C Include diffraction data Bioloaical unii Import umport structure tile Browse Preprocess the Workspace structure Align to Selected entry Opps Assign bond orders Add hydrogens Remove original hydrogens Create zero order bonds to metals Create disulfide bonds Cl Convert selenomethionines to methionines _ Fill in missing side chains using Prime OFI in missing loops using Prime X Cap termini 5 A from het groups Preprocess View Problems Protein Reports Ramachandran Plot Imported 1su4 Reset Close Help 5 Change the view to ribbon view in the workspace and orient the protein similar to what can be seen in Figure 2 6 which is the standard way of looking at membrane proteins with the transmembrane bundle aligned along the vertical axis April 2011 D E Shaw Research 27 Desmond Tutorial Figure 2 6 The 1su4 structure in standard orientation Preparing a Desmond simulation with the System Builder Maestro Project Edit View Workspace Tools Applications zz oe uram E g P k KR A WX K H SF KH Select Undo Redo Delete Sketcher AddH Transform Adjust ae X X X a X cH 2 oo o gt Wire CPK Ball amp Stick Tube T
24. Table Open the Project Table The Trajectory Player can be launched from the Project Table Note the blue T in the Title column in the Project Table as shown in Figure 6 1 Figure 6 1 Launching the Trajectory Player 88 NOTE NOTE ed Project Table Scratch Project Table Select Entry Property Group ePlayer 4 A Y I ep 2D E Find Replace Sort Plot Import Export Columng Selectonly 2D Structure 2D Viewer Click T to open the Trajectory Player Entries 1 total 1 shown 1 selected 1 included Groups 0 total 0 selected Click T to open the Trajectory Player The Trajectory Player is shown in Figure 6 2 and the associated Maestro workspace view can be seen in Figure 6 3 The Trajectory Player has two sets of options for frame control and display proper ties the best way to learn about these options is to experiment with them The Tra jectory Player is fully documented in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 In most cases you do not want the entire system to be displayed when for example visually inspecting the conformational changes of a protein molecule along the trajec tory The Trajectory Player recognizes Maestro s current display settings which means that you can select deselect any set of atoms for display using the Workspace gt Display menu options and you can also render the atoms in any way you want The Trajectory Player wi
25. View Workspace Tools Applications Workflows Scripts Window Help a FF Sw amp FH 2 PDB S na ge e U taam Be FT FOG AS Open Save As Import Export Table 2D Viewer Lig int GetPDB PrepWiz Ft Fog Enhance RotateX Rotate Y Tilg R Rm mo xX AHCS T a 6 Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image New Scene lt w X X X E A X amp ce 6 0 O gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color voy zo Y X X X Find Residue number y 219 N P 0 of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Suitable membrane placement for 1su4 NAAT i Atoms 0 62 15799 Entries S 1 13 Res 1116 Chn 2 Mol 117 Chg 23 XMEAAHSKSTEECLAYFGVSETTGLTPDOVKRHLEKYGHNELPAEEGKSLWELVIEQF OLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLIL IANA IVGVWQERNAENA IEALKE YEPEMGKVYRADRKSVORIKARDIVPGDIVEVAVGDKVPADIRILS IKSTTLRVDOS ILTGESVSVIKHTEPVPDP g Zz RAVNODKKNMLFSGTN IAAGKALGIVATTGVSTE IGKIRDOMAATEODKTPLOOKLDEFGEOLSKV ISLICVAVWLINIGHFNDPVHGGSWIRGAIYYF 6 ISUJ A KIAVALAMIBIBNGLPAVITTCLALGTRRMAKKNA IVRSLPSVETLGCTSV ICSDK1TGTLTINOMSVCKMF I IDKVDGDFCSLNEFSITGSTYAPEGEV LKNDKP IRSGOFDGLVELATICALCNDSSLDFNETKGV YEKVGEATE TALTTLVEKMNVENTEVRNLSKVERANACNSV IROLMKKEF TLEFSRDRKSM SVYCSPAKSSRAAVGNKMFVKGAPEGV IDRCNYVRVGTTRVPMTGPVKEKILSV IKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSREMEYETDLTF VGVVGMLDPPRKEVMGS IOLCRDAG IRV IMI TGDNKGTAIA ICRRIGIFGENEEVADRAY1
26. and single atom mutation in a ring structure From Maestro you can visually specify the fixed and variable parts of a molecule that are sub jected to FEP calculations and then store the atom correspondence map which defines dual topologies in the Maestro mae file Ligand mutation the most common FEP calculation is illustrated in Figure 5 1 using a typical scenario The figure shows a graphical representation of the soluble form of the human urokinase plasminogen activator receptor SUPAR PDB code 2fd6 and the ZINC 01538934 ligand The protein structure has been processed using the Protein Preparation Wizard as described in Tutorial Steps on page 3 and the ligand was docked using Schr dinger s Glide application as part of a virtual screening experiment on the ZINC database http zinc docking org The ligand is rendered in a tube representation in the sUPAR active site with green carbon atoms and ball and stick representation April 2011 D E Shaw Research 61 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 1 FEP Example Ligand mutation J iiaestro j 5 x Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help an R z any a PDB ga ae ome De g Y S58 A 6S Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile Le A C m X AHE Ra Select Undo Redo Delete Sketcher Add Transform
27. are ACE on the N terminus and NMA on the C terminus Delete waters In general select this option only if you have a reason to remove crystal waters Set the distance to a small value to remove all water molecules Het groups refers to atoms that are labeled HETATM in a PDB file anything that is not a protein residue or water Do not delete waters for this Tutorial exercise NOTE In most cases crystal waters should not be removed from the interior of the protein mol ecule or near the protein surface These water molecules are crucial structural compo nents of the protein and cannot be adequately reproduced by the algorithm used to solvate the system later on 13 Click Preprocess to execute the first phase of the protein preparation tasks 8 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Setup takes only a few seconds to complete The Protein Preparation Wizard displays the chains waters and het groups as shown in Figure 1 8 Figure 1 8 Protein Preparation Wizard Preprocessing stage The added capping groups are shown in wire frame representation April 2011 ET TET EEE B Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help E Rm amp ye Utas a kY Open Save As Import Export Table 2D Viewer Lig Int GetPDB_ Prep Wiz Z 5 z mw A xXx KH Or HM ded amp A J Protein Preparation Problems 77777777A AAAA Select Undo Redo De
28. command at the command line SSCHRODINGER run SSCHRODINGER utilities system_builder my_setup csb where my_setup is the file name given to Write Run the system_builder script with the help command argument instead of the csb file to see advanced options Setting Up Membrane Systems April 2011 The Setup Membrane panel as shown in Figure 2 4 can be used to embed a membrane pro tein structure in a membrane bilayer In this procedure a template consisting of an equili brated membrane including the accompanying water is used to generate a large enough region to encompass the protein Using the Setup Membrane panel you can posi tion the protein within the membrane using a semi automated procedure D E Shaw Research 25 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 4 Membrane setup in the System Builder 26 Membrane model Predefined POPC 300K v Custom Browse Transmembrane atoms ASL optional _ select Set to Helices Place Automatically Place on Prealigned Structure Adjust membrane position Save Membrane Position Load Membrane Position Pok X cancel f V7 System Builder Set Up Membrane j x As a real life example we can consider the calcium ATPase protein 1su4 Follow the pro cedure below to prepare this protein for membrane simulation in Desmond To setup the 1su4 m
29. details about the configuration settings for FEP simula tions see the Desmond User s Guide and the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 for a full account of this topic D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Setting Up an FEP Calculation 6 There are several ways to run the FEP simulation Write your own Desmond configuration file and run the FEP simulation from the command line See Running FEP Simulations from the Command Line on page 70 for instructions to run the FEP simulation from the command line This is the most flexible but least automated approach Use Maestro to generate any non default Desmond configuration file and run the FEP simulation from the command line See Using Maestro To Generate A Des mond FEP Configuration File on page 68 for instructions on using Maestro to generate the configuration file See Running FEP Simulations from the Com mand Line on page 70 for instructions to run the FEP simulation from the com mand line Run the FFP simulation directly from the Ligand Functional Group Mutation by FEP panel by clicking Start The workflow defined in the msj files is automatically executed This workflow has a short description shown under the Plan Calculation tab shown in Figure 5 6 essentially system setup with System Builder is automat ically performed and all required Desmond simulation
30. e g artifacts of crystallization set correct bond orders add hydro gens detect disulfide bonds and fill in missing side chains or whole residues as necessary Refine the prepared structure file During this step you analyze the choices made by Maestro s Protein Preparation Wizard and manually change protonation and tauto meric states of variable residues and when present of ligands and co factors If your system is a membrane protein immerse the protein in the membrane Generate a solvated system for simulation Distribute positive or negative counter ions to neutralize the system and introduce additional ions to set the desired ionic strength when necessary Let Maestro assign OPLS AA force field parameters to the entire molecular system alternatively assign force field parameters external to Maestro with Desmond s Viparr utility program which provides access to a variety of widely used force fields Configure simulation parameters using the Desmond panel in Maestro or edit the Desmond conguration file Run the simulation from Maestro or from the command line 10 Analyze your results using the Trajectory Viewer and other analysis tools This process is illustrated in Figure 1 1 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 1 Simulation process Structure Preparation fret H Prepare the structure Structure file for simulation gt File Mae Structure File E Refin
31. fers p a nrram BE g P Open Save As Import Export Table 2D Viewer Lig int GetPDB Prep Wiz ff Be M 9 X K H E A O g ta Q A 35 ale Fit Fog Enhance Rotate X Rotate Y Tile d 5 Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene c 3s Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X xv y x X 7 Y Find Atom number Atoms 0 147743 147743 Entries 1 3 A z ME Project Edit View Workspace Style Saved Views Display Atoms 5 Pa 0 of 0 Res 32760 Chn 3 Mol 31968 Chg 0 ft Representation Labels Build Fragments A elx Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Figure 2 25 OPM transmembrane hole in the POPC bilayer for 1su4 April 2011 P a III I I Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help E i od PDB Ra aje ma ee iy m E3 fat y CE Q A Sy as Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile Th s Create Entry Clear Save Image New Scene Q Q e 0 22 gt A Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X x y x Y X X Y mM XI K Hue amp
32. layer is the gap between the water layer that is part of the POPC model and the extra water layer which was added to the system to satisfy the boundary conditions This is expected since the system is put 36 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder NOTE Setting Up Membrane Systems together from two different pre equilibrated boxes of a solvated lipid bilayer and plain solvent respectively The gap should go away after a relatively short equilibration period However membrane systems should be equilibrated for an extended period of time to resolve the large hole that was carved out of the lipid bilayer to accommodate the trans membrane part of the protein The hole is shown for the 1su4 structure in Figure 2 17 The protein in the simulation box in Figure 2 16 is positioned so that the head of the pro tein is shifted to the top of the simulation box This is the result of a visual artifact dis cussed in Defining the Simulation Box on page 22 System Builder puts the center of gravity of the solute at the center of the simulation box As a consequence fairly non spherical systems will appear to shift toward one side of the simulation box Membrane systems are extreme cases resulting in the view on Figure 2 16 This may not be ideal from a visual perspective but in terms of periodic boundary conditions this is perfectly ade quate Figure 2 16 Final simulation system for 1su4 Apri
33. molecule you ll notice that the molecule chooser at the top of the Molecule File Browser now points to your newly created molecule If you create more new molecules using different cms files select New Molecule from the molecule chooser and repeat the steps above Otherwise to append snapshots to this molecule from a trajectory click Browse again and navigate to the location of the dtr file you wish to load Since dtr trajectories are stored as directories rather than ordinary files clicking on a DTR trajectory will take you inside of a directory Figure 7 3 You should see a file called clickme dtr Click on it and VMD will figure out that you wanted to load the frames within the direc tory containing the clickme dtr file April 2011 D E Shaw Research 97 Desmond Tutorial System Setup and Trajectory Analysis Using VMD Figure 7 2 Loading the Maestro file Load fles for NewM esIE Click Browse and select Filename fiond_job_files 4pti_desmond_run outcms Browse your structure file Determine ERDE M o Maestro file will appear 1 p eF automatically in the file Fiat e SE type field Click Load a Fi Ea Volumetric Datasets Load in background Load all at once Figure 7 3 Loading trajectory data v Choose a molecule file ax Show All Files v Favorites X Al E a Select the clickme dtr file ___ pypsmerere to load the frames within S
34. project Incorporate Append new entries v Job Enter a name for the simulation job N One job to submit for 1 simulation Name 4pti_Desmond_md_job Select the host where the job should run usually ee i localhost on a j The system will be domain decomposed as follows standalone workstation AEREN aes cil a x 1 y 2 z 2 Actually needs 4 CPUs simulation Set the number of CPUs i z and domain decomposidon asnooded ea Cancel Click Start 2 Select Append new entries from the Incorporate option menu in the Output area to indi cate that results of the Desmond simulation should be added to the current Maestro project 3 In this example the job will run on localhost which is typically a standalone work station using 4 CPUs with a domain decomposition the number of blocks into which the simulation box will be split in the X Y and Z directions of 1x2x2 For large scale simulations Host is usually a Linux cluster with dozens to hundreds of CPUs 4 Click Start The Desmond simulation process begins Running Simulations from the Command Line Given a valid cms structure file and corresponding cfg conguration file the command line syntax for running Desmond jobs is as follows SSCHRODINGER desmond HOST lt hostname gt exec lt desmond_task gt P lt cpu gt c lt jobname gt cfg in lt jobname gt cms In case a job has to be restarted from a checkpoint file replace
35. right click on atom bond and hold menu 22 Click the lons tab The lons panel appears as shown in Figure 1 14 14 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 14 lons tab in Desmond System Builder April 2011 NOTE NOTE m System Builder 777 Click the lons tab ons Excluded region Exclude ion and salt placement within A of Select Clear lon placement None Select Neutralize Neutralize by adding 6 Cl ions Recalculate Add 4 Advanced ion placement sesencsSe pce f Add salt Enter 0 15 in the satt concentration 015s M Salt concentration Salt positive ion Na box Salt negative ion Cl Force field opLs2005 7 Click Start _ _Start Write J Reset_ Close Help 23 For lon placement select Neutralize 24 In the Salt concentration box enter 0 150 This will add ions to the simulation box that represent background salt at physiological conditions Membrane systems can also be built with the System Builder but this is deferred to Set ting Up Membrane Systems on page 25 which covers membrane setup steps in detail 25 Click Start to start building the solvated structure You will need to provide a job name and choose a host on which to run the System Builder job When complete the sol vated structure in its
36. sample simulations and information about Desmond work shops https sites google com site desmondmdusers Be sure to check the Known Issues file already included with the Desmond Maestro distribution for undocumented issues and problems with the current release Schr dinger also provides an extensive searchable knowledgebase with numerous Des mond related articles http schrodinger com kb Schr dinger s Desmond documentation includes the Quick Start Guide and the Desmond User Manual SCHRODINGER docs desmond des30_quick_start pdf and SCHRODINGER docs desmond des30_user_manual pdf The documentation is also available by choosing Help gt Manuals Index in Maestro Maestro documentation can be found online at www schrodinger com and context spe cific online help can be brought up in any Maestro panel which has a Help button The complete Maestro documentation set includes SSCHRODINGER docs maestro mae92_command_reference pdf SSCHRODINGER docs maestro mae92_tutorial pdf SSCHRODINGER docs maestro mae92_user_manual pdf The full ASL atom specification language documentation can be found in SSCHRODINGER docs maestro mae92_help misc asl html D E Shaw Research 111 Desmond Tutorial 112 The documentation of Prime can be found at S SCHRODINGER docs prime pri30_quick_start pdf and SSCHRODINGI ER docs prime pri30_user_manual pdf D E Shaw Research Documentation Resources
37. the c and in options with restore and the name of the checkpoint file SSCHRODINGER desmond HOST lt hostname gt exec lt desmond_task gt P lt cpu gt restore lt jobname gt cpt where e lt desmond task gt can be either minimize to run a simple minimization mdsim xemd for replica exchange job to run an MD simulation including FEP jobs described in Preparing Free Energy Perturbation and Metadynamics on page 61 or vrun to run the vrun trajectory analysis tool see the Desmond User s Guide for information about vrun Note that vrun is the engine of the Schrodinger Simulation Event Analysis tool which can be accessed from the Applications gt Desmond menu e lt jobname gt is the name of the job 56 D E Shaw Research April 2011 Running Desmond Simulations Running Simulations from the Command Line April 2011 NOTE NOTE e lt hostname gt is the name of the compute host which can also be the name of a queue on a cluster e lt cpu gt species the number of CPUs you want each Desmond simulation subjob to use This should be 1 for running the serial version of Desmond for example to quickly test on your workstation whether your job will start at all or a power of 2 The number of CPUs requested for a restore job must be the same number of CPUs used with the job that saved the checkpoint file You can restart a Desmond MD simu lation job from the Molecular Dynamics panel as well as shown in Figure 3
38. the simu lation parameters for the production run Note that the actual configuration file read by Desmond is called 4pti_Desmond_md_job out cfg which is sub ject to postprocessing the original cfg file Apti_Desmond_md_job cms The input structure file for simulation including the force field parameters 4pti_Desmond_md_job msj The multisim command script describing the details of the equilibration stages 4pti_Desmond_md_job_multisim log The log file of the master multisim job 4pti_Desmond_md_job out cms The output structure file the last frame of the trajectory 4pti_Desmond_md_job_2 out tgz Compressed tar files containing all the information Apti_Desmond_md_job_3 out tgz about the relaxation equilibration stages 4pti_Desmond_md_job_4 out tgz Apti_Desmond_md_job_5 out tgz 4pti_Desmond_md_job_7 out tgz 4pti_Desmond_md_job_8 out tgz 4pti_Desmond_md_job log The log file of the production simulation 4pti_Desmond_md_job ene The instantaneous energy terms of the production run are stored in the ene file April 2011 D E Shaw Research 19 Desmond Tutorial 20 Table 1 1 Simulation files Desmond Tutorial File Purpose Apti_Desmond_md_job_trj Apti_Desmond_md_job out idx Apti_Desmond_md_job_simbox dat Apti_Desmond_md_job cpt The trj file is in fact a directory which contains the trajectory snapshots in multiple binary files How ever from an analysis point of view this directory can be conside
39. to the same frame prol0 atomsel protein frame 10 Select the waters near the protein from molecules 0 and 1 wat0 atomsel water and same residue as within 5 of protein molid 0 watl atomsel water and same residue as within 5 of protein molid 1 D E Shaw Research 105 Desmond Tutorial 106 System Setup and Trajectory Analysis Using VMD As illustrated above the atomsel type takes three arguments all of which are optional e selection default a11 This is the selection predicate The selection language is described in full in the VMD User s Guide e molid default 1 The molid is the molecule associated with the selection and never changes The default molid of 1 means the top molecule at the time that the selection was created If the top molecule happens to change after the selection is created for instance when a new molecule is loaded the molid does not change If a molecule gets deleted from VMD s workspace all associated atom selections are invalidated e frame default 1 The frame is the index of the snapshot referenced by the selec tion The default value of 1 means that the selection should reference whatever the current frame happens to be A frame value of 0 or higher means the selection always refers to the same frame even if the current frame changes If the frame ref erenced by selection does not exist then the last frame in the molecule is used You can get and set the fram
40. total 0 12 p a Recording interval ps energy 1 2 Enter 0 12 in the Simulation time box elapsed 0 0 trajectory 4 8 Ensemble class NPT Temperature K 300 0 Select Relax model Surface tension bar A 40000 system before simulation l Relax model system before simulation Pressure bar 1 01325 Relaxation protocol Browse Advanced Options Desmond Developed by D E Shaw Research Click Start start Read Write Reset Close Help 27 Import the model system into the Molecular Dynamics environment select either Load from Workspace or Import from file and select a cms file and then click Load The import process may take several minutes for large systems For this example select Load from Workspace 28 In the Simulation time box set the total simulation time to 0 12 ns 29 Select Relax model system before simulation This is a vital step to prepare a molecular system for production quality MD simulation Maestro s default relaxation protocol includes two stages of minimization restrained and unrestrained followed by four stages of MD runs with gradually diminishing restraints This is adequate for most simple systems you may also apply your own relaxation protocols by clicking Browse and selecting a customized command script For more details see Running MultiSim jobs from the Command Line
41. 1 on page 52 Select Import from file and browse to select the checkpoint file Also note that the restore mechanism can readily be used for continuing a completed simulation if you simply want to extend the trajectory but make sure to specify the total simulation time of the extended simulation not the additional time For example if you want to extend a 100 ns simulation by another 100 ns simulation time should be set to 200 ns Advanced users should consider the following e The Desmond driver in the Maestro environment tries automatically optimizing cer tain configuration parameters and therefore the actual cfg file called your_jobname out cfg that is used by Desmond itself may not be identical to the original cfg file that you prepared The differences can be safely ignored most of the time but in some cases you may want to run Desmond with the exact parameters given in the cfg file To turn off internal optimization launch Desmond from the com mand line with the noopt argument SSCHRODINGER desmond noopt e By default Desmond applications are run in single precision Use the dp option to switch to double precision This is only recommended for debugging purposes because of the performance penalty caused from using double precision There is a particularly useful command line script that can automatically generate reasonable Desmond configuration settings to facilitate efficient force computations including non power of tw
42. A HOH 151 Initial 68 A HOH 152 Initial 69 C A HOH 153 Initial 70 A HOH 154 Initial 71 A HOH 155 Initial Atoms 3 751 1081 Entries 1 4 Res 120 Chn 1 Mol 61 Chg 6 72 A HOH 156 Initial middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on ato 73 A HOH 157 Initial Add Orientation Sort By State Pick to locate species Slide the list down to the water section and click entry 69 to select HOH153 The view in the Maestro workspace zooms in and centers on the close contact as shown in Figure 1 10 Click the Restore View icon next to the Optimize button to zoom out 10 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 10 Protein Preparation Wizard Interactive H bond optimizer E GEE ex Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help shah bs Be SSS A amp amp Open Save As Import Export Table 2D Viewer Lig Int GetPDB PrepWiz Fit Fog Enhance Rotate X RotateY Tile ma x Kx CC HS amp 4 amp Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Savelmage NewScene Vi r saa i Dd Dd X X 00 00 gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color v v y vy x Y Fit a AB You can set the pH for H i el bond analysis PH neut
43. Amber Molecular Dynamics simulation input files to the Desmond environment Generating Force Field Parameters with Viparr Viparr is a Python script that reads a cms or mae file and writes another cms file which has all the force field parameters required to run a Desmond simulation Viparr can assign force field parameters from a variety of well established force fields and water models Viparr force field assignment is template based This means that unlike force field servers e g Schrddinger s OPLS AA server that can generate parameters for various atom types derived automatically from the molecule s topological structure Viparr is designed to find templates such as an entire residue in cms files and assign the appropriate force field parameters by looking at a template database associated with a particular force field The D E Shaw Research 47 Desmond Tutorial NOTE 48 Finishing Preparations for Desmond Simulation resulting parameters are guaranteed to be identical with those of the published authen tic force field When Viparr begins it wipes out all previous force field information from the input cms file Therefore it is efficient to build the simulation system using System Builder and then perform post processing on the cms file with Viparr to assign the desired force field parameters The Viparr script is called viparr py and basic help on its usage can be obtained via the command line output for version 1
44. Desmond Tutorial Desmond Version 3 0 Document Version 0 6 April 2011 D E Shaw Research Notice The Desmond Tutorial and the information it contains is offered solely for educational purposes as a service to users It is subject to change without notice as is the software it describes D E Shaw Research assumes no responsibility or liability regarding the correctness or completeness of the information provided herein nor for damages or loss suffered as a result of actions taken in accordance with said information No part of this guide may be reproduced displayed transmitted or otherwise copied in any form without written authorization from D E Shaw Research The software described in this guide is copyrighted and licensed by D E Shaw Research under separate agreement This software may be used only according to the terms and conditions of such agreement Copyright 2008 2011 by D E Shaw Research All rights reserved Trademarks Ethernet is a trademark of Xerox Corporation InfiniBand is a registered trademark of systemI O Inc Intel and Pentium are trademarks of Intel Corporation in the U S and other countries Linux is the registered trademark of Linus Torvalds in the U S and other countries All other trademarks are the property of their respective owners April 2011 Preface Intended Audience This tutorial is intended for computational chemists using Desmond in setting up and running molecular dyna
45. Energy Perturbation and Metadynamics Figure 5 17 Butyl group superposed with original side chain The original side chain The modified side chain April 2011 Other Types of Mutations Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help oR ht De E xe PF FHSS A F Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Ft Fog Enhance RotateX Rotate Y Tile min X KH NS amp J GH amp Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene g ce 2 6 O D F Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X voy d X X d i e wz Z R g SA ea W A kg tA o amp Ss Q Dr Draw Set Element Bond Order Bond Order Formal Chg Formal Chg Move R S Cleanup Sculpt Find Atom number bd P O of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Other Types of Mutations You can also perform these mutations from the Applications gt Desmond menu D E Shaw Research Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu Protein residue mutation can be used for two different types of calculation With one calculation the difference in free energy is computed for a ligand
46. FEP simulations MultiSim requires special mae files for input instead of cms files These mae files are generated by the FEP panels ligand mutation protein residue mutation ring atom mutation and absolute total free energy calculation and include the dual topology structure of the mutations The FEP MultiSim script will explicitly call the System Builder to prepare the solvated systems and gener ate the OPLS AA force field parameters To apply non default FEP parameters or to change the number of Lambda windows add the c config_file option to the command syntax where config_fileisa Desmond FEP conguration file that was generated by the FEP panels as shown in Figure 5 7 on page 69 Note that this conguration file will be used throughout the msj workflow to make sure that all minimization and MD runs use the same settings for consistency Also note that FEP parameters like any other Desmond configuration setting can always be defined directly in the MultiSim script and those values set in the msj file take prece dence In particular you can cut and paste the FEP block from the cfg file defining the custom lambda schedule inside the desmond block below in the stock msj file that is generated by the ligand residue ring atom FEP panels task task desmond auto set_family desmond checkpt wall_interval 7200 0 checkpt write_last_step no fep lambda D E Shaw Research April 2011 Preparing F
47. GREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLO Jobs 0 0 f middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu NOTE You may want to position two or more different membrane proteins e g for mutagene sis studies in a bilayer in exactly the same way Of course this would be virtually impossible to do trying to reproduce the same manual adjustments The Set Up Mem brane dialog box in the System Builder provides a convenient way to automate this proce dure Any time you are satisfied with the membrane placement the net translation rotation transformation matrix can be saved in the project entry by simply clicking Save Membrane Position in the Set Up Membrane dialog box see Figure 2 11 on page 32 Then for any subsequent protein you can simply click Load Membrane Position to position the entry according to the saved transformation matrix This way all proteins will be placed in the membrane in exactly the same position and orientation 11 Finally click OK in the Set Up Membrane dialog box and click Start in the System Builder panel to start the membrane system setup For 1su4 the setup procedure should take 6 8 minutes The resulting simulation system is shown in Figure 2 16 on page 37 For better visualization the protein is shown as a CPK model and the lipid bilayer is highlighted in green NOTE The visible gap at the top and bottom of the lipid
48. H NH4 group To restore the default methyl substitution group you can click the Reset column in the Ligand Functional Group Mutation by FEP panel April 2011 D E Shaw Research 79 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 16 Unfavorable contacts removed hd Maestro Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help a EE amp Fa sn PDB g Ba eje ao praam EE g Y 72 S aA S Open Save As Import Export Table 2DViewer Lig int GetPDB PrepWiz Ft Fog Enhance RotateX RotateY Tile A pa 4 a mw OY X KH SF SM h d a Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene E A X sce b oOo 8 9 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color x y vO X X Y A 5 f R 3 A gt Oa Ca W ay A e G 8 b SN Dr Draw SetElement Bond Order Bond Order FormalChg FormalChg Move R S Cleanup Sculpt Find Atom number vi N P O of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Only allowed close contacts remain The unfavorable contacts have been removed Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 80 D E Shaw Research April 2011 Preparing Free
49. Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz mo x KH eC A amp E Create Entry Clear Save Image New Scene Select Undo Redo Delete Sketcher AddH Transform Adjust X X X X Q o D 2 Display Sel Display Only Also Display Undisplay Within H i s 5 Scoe t oOo 9S 9 Ribbon Wire CPK Ball amp Stick Tube ThinTube Color Scheme Color X x y X X X Y Find Atom number xe N P O of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Workspace view of the Trajectory Player Jobs 0 0 Atoms 0 14026 14026 Entries 1 1 Res 4425 Chn 2 Mol 4396 Chg 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu Performing Simulation Quality Analysis Maestro can also perform basic quality analysis Launch this tool from the Applications gt Desmond gt Simulation Quality Analysis The quality analysis panel appears as shown in Figure 6 4 90 D E Shaw Research April 2011 Visualization and Analysis using Maestro Performing Simulation Quality Analysis Figure 6 4 Simulation Quality Analysis panel Select the energy EETL file Job base name folossva Playground build16 Desmond_Tutorial 0 6 4pti_Desmond_md_job_long Browse Plot Block length for averaging 10 0 ps H g z Click Analyze E Simulati
50. KEFTLEFSRDRKSM 6 ISU4 A SVYCSPAKSSRAAVGNKMFVKGAPEGV IDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTF lt 6 ISU4_A VGVVGMLDPPRKEVMGS IQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLO middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 10 Select Adjust membrane position in the Set Up Membrane dialog box as shown in Figure 2 11 on page 32 At this point you should be able to translate and rotate the membrane model in the workspace relative to the protein structure Moving the membrane relative to the protein structure is termed the local scope for transforma tions However for a better view you will probably want to translate rotate the system as a whole as well This is called the global scope and you can switch back and forth between the local and the global scopes by repeatedly clicking Transformations called out in Figure 2 14 With only a few translations and rotations switching between the local and global scopes you should be able to place the membrane in a suitable start ing position After applying manual transformations you should place the membrane similar to that shown in Figure 2 15 April 2011 D E Shaw Research 35 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 15 Adjusted position of the membrane for 1su4 Maestro Project Edit
51. Kil J Update Delete Clean Up Postmortem Details File Files ___ Job summary Name 4pti_Desmond_md_job Lo 4pti_Desmond_md_job_multisim Program multisim OSH spt Desmond_md_job multisim_ Bee Status finished ug R Status incorporate i aes ERE AOU ETAZ Status updated 2011 03 12 14 29 41 4pti_Desmon _job_2 out tgz Job Host drdws0086 nyc desres deshaw com 4pti_Desmond_md_job_3 out tgz Job Directory 4pti_Desmond_md_job_4 out tgz d en maestro 0 kolossva 4pti_Desmond_md_j ob apti Desmond mi job saut tae be a a ate se 15 08 32 ol ndeda je a i Sia Desmona wale 00 7 dut tyz Jobrd drdws0086 0 4d7bc9a5 4pti_Desmond_md_job_8 out tgz Parent JobId None Output 4pti_Desmond_md_job_trj Sub JobId 1 drdws0086 0 4d7bc9e6 ee Desmond_md_job out idx Sub JobId 2 drdws0086 0 4d7bca66 timekeys _ Sub JobId 3 drdws0086 0 4d7bcacb Sub JobId 4 drdws0086 0 4d7bcbc9 ea Sub Jobrd 5 drdws0086 0 4d7bcc92 ae Metadata Sub JobId 6 drdws0086 0 4d7bcd57 E Desmond_md_job ene Sub JobId 7 drdws0086 0 4d7bce74 Output not_hashed Last updated Sun Mar 13 16 56 00 2011 upie clickme dtr Output 4pti_Desmond_md_job cpt 4pti_Desmond_md_job in cms Onepu 4pti_Desmond_md_job out cms zJ Close Help In this case the file list includes the following in Table 1 1 below Table 1 1 Simulation files File Purpose 4pti_Desmond_md_job cfg The Desmond conguration file which has
52. LKNDKP IRSGOFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIROLMKKEFTLEFSRDRKSM 6 ISU A SVYCSPAKSSRAAVGNKMFVKGAPEGV IDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTF rIsua_k VGVVGMLDPPRKEVMGS IOLCRDAG IRV IMI TGDNKGTA IA ICRRIGIFGENEEVADRAYTGREFDDLPLAEOREACRRACCFARVEPSHKSKIVEYLO middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu The blue blob shows the excluded region and the selected candidate residues are highlighted by red spheres The positive counterions will be placed close to the red spheres which mark the atoms within the residues that have the largest magnitude partial charge Also note that the residues that constitute the excluded region are highlighted in blue in the sequence viewer In many cases you may want to place only a few counterions at particular locations and distribute the rest of the charges in a truly random fashion Follow the steps below to achieve this goal a Set the Solvent model to None Figure 2 2 on page 22 and instead of neutralizing explicitly add the number of counterions to the system that you want to place at particular locations Select Add in Figure 2 3 on page 24 Apply the advanced ion placement procedure above to place this subset of counterions in the desired locations Run the System Builder to generate this intermediate system with no solvent a
53. Once you have arrived at this point you are ready to prepare the structure for simula tion Just having a molecular model in the workspace is not enough to perform molec ular mechanics dynamics calculations You must prepare the protein model so that it corresponds as closely as possible to the biological system you are studying From this view it is clear that there are no hydrogen atoms in the protein structure Moreover there might be ill defined bond orders protonation states formal charges tautomerization states disulfide bonds and so on The red dots shown in the work space represent crystal waters All of these issues must be resolved before we can per form simulation calculations There are two methods of correcting these issues using Maestro s general purpose molecular structure editor or the Protein Preparation Wizard which is a very useful automated tool for protein structure preparation For this tutorial we will use the Protein Preparation Wizard April 2011 D E Shaw Research 7 Desmond Tutorial Desmond Tutorial 11 Select Workflows gt Protein Preparation Wizard NOTE Note the pop up warning that Epik and Glide are not available to academic users free of charge but these tools are generally not necessary to setup Desmond simulation The Protein Preparation Wizard panel appears as shown in Figure 1 7 Figure 1 7 Protein Preparation Wizard panel Protein Preparation wara IE Job prefix prepwizard Displa
54. Scheme Color a A X v v Y PlOof 0 Fit y Atoms Representation Labels Build Fragments snow Ribbons for All Residues Show Ribbons for Selected Residues Show Ribbons for Displayed Residues Display Atoms Undisplay Atoms Display Side Chains and Portion of Backbone Only Delete Ribbons Secondary Structure Chain Name CA Atom Color Residue Charge Residue Property Residue Type Residue Position Entry Constant Color Switch from ribbon view to ball and stick view by clicking Ribbons and selecting Delete Ribbons from the option menu that appears as shown in Figure 1 5 Next as shown in Figure 1 6 double click Ball amp Stick and finally click Color Scheme to color the carbons in the structure green D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 6 Changing from ribbon to ball and stick view iv Maestro l wat ox Ea B ane gt a W W 3 E x F 2 Open Save As Import Export Table 2D Viewer Lig int GetPDB Prep Wiz mM OA X A tH oF HS fh Create Entry Clear Save Image New Scene Double click Ball amp Stick Find Residue number Project Edit View Click Color Scheme Custom Carbons Green Atoms 0 514 514 Entries 1 1 Res 118 Chn 1 Mol 61 Chg 6 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu
55. Using VMD Centering trajectories To generate a continuous trajectory view with the protein centered in the primary simu lation box load your trajectory into VMD and try either of the following commands from VMD s Tk console Extensions gt Tk Console pbc wrap centersel protein center com compound res all pbc wrap center bb centersel protein sel not protein compound res all You may have to superimpose all frames of the trajectory onto a selected frame in order to center the view in the main VMD graphics window To do so select VMD gt Extensions gt Analysis gt RMSD Trajectory Tool and select the Align option Note that the transformed trajectory can be written to disk for further analysis Writing structures and trajectories Modified structures or trajectories can be written back out to disk for further analysis or as input to simulation preparation There are two distinct methods for writing out coor dinates The first method for writing coordinates and structure is the molecule write command molecule write molid dtr trajectory dtr waitfor 1 The molia filetype and filename are required parameters The wait for option indi cates how many frames should be written before returning from the command you will almost always want to use 1 You can also specify a range of frames to be written just like the molecule read command molecule write molid dtr trajectory dtr beg 100 end 1
56. VMD s sophisticated tools to analyze Desmond trajectories This section assumes a Unix Linux environment and basic familiarity with VMD If you re just getting started with VMD a number of excellent tutorials already exist and can be found on the VMD home page http www ks uiuc edu Research vmd current docs html tutorials The VMD Python Interface The Python interface can be accessed from either the console the terminal from which you launched VMD or from an Idle window that runs inside of VMD preferred To ini tiate the Python interface in the console simply type gopython at the vmd gt prompt To launch the built in Idle window you ll need to set your PYTHONPATH properly as described in the Desmond installation instructions The console command to launch the Idle window is gopython command import vmdidle vmdidle start D E Shaw Research 95 Desmond Tutorial 96 NOTE System Setup and Trajectory Analysis Using VMD You may wish to copy this command into your vmdrc so that you open this window every time you launch VMD Once you have a Python prompt at either the console or the Idle window you re ready to start using the VMD Python interface In Python classes and functions are organized into modules Some modules are pro vided by the Python interpreter when you launch Python while others are discovered at runtime and loaded from separate files When you access Python from within VMD the VMD executable prov
57. You can hide toolbar buttons on any toolbar if you do not use them Right click the toolbar and choose Customize Each toolbar can be shown with icons only with text labels or text only Right click the toolbar and choose the Style menu D E Shaw Research April 2011 e Note that application and option panels pop up with a noticeable delay However this only happens when you open a panel for the first time Within the life cycle of a Mae stro session subsequent opening and closing of such windows is instantaneous Format Conventions April 2011 Command lines appear in a monospaced font SSCHROI D INGER maestro File names are bolded within text equil cfg Menu selections you must make for the tutorial are bolded For example Select Project gt Get PDB Screen elements such as panel titles option names or button names appear in special text For example Click ButtonName D E Shaw Research iii Desmond Tutorial iv D E Shaw Research April 2011 Contents PIrelace ss ows bec atah aee Gait be Cees we Se OU ae es es ee ee i Intended Audience oann a e a T e E ee i PREPEGUISILES satria aa a r Geis AE e E nae a Ate ean Eee Le ae Mass i About this Guide 4 soras be i bie eg a ey Sk ES Sl eh oe ek ii Release Notes na amp amp e gdh ies eo ee Aten Ee G a hans ate Moe bd at ii Format Conventions oea 0 0 ea e e ee iii 1 Desmond Tutorial i iisi62 0 2 tte Baa Bee Bs Ble CES Ee oe Ree a
58. age 75 The resulting side chain is a butyl group as shown in Figure 5 13 Close the Build panel 76 D E Shaw Research April 2011 Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help v uram Fe FP Fes A Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Ft Fog Enhance RotateX Rotate Y Tile mO x RHES h H 8 Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Preparing Free Energy Perturbation and Metadynamics Adjusting the Conformation of the Mutant Figure 5 13 The butyl substitution group shown in the workspace r Metro EEE Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help e Uram E Kx F FUSS A Open SaveAs Import Export Table 2D Viewer Lig int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tiig R 2 p 4 wa X KH eS SS amp d GH 5 Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene Ce N ece a oo 8 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X voy x X X Zk amp o 6 SNFA Draw SetElement Bond Order Bond Order FormalChg FormalChg Move R S Cleanup Sculpt Find Atom number D NPO of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labe
59. al Preparing Free Energy Perturbation and Metadynamics This page left intentionally blank 86 D E Shaw Research April 2011 6 Visualization and Analysis using Maestro April 2011 Overview Maestro provides three basic visualization and analysis tools Maestro s Trajectory Player is similar to the ePlayer found in the Project Table but it is specifically designed to nicely ani mate Desmond trajectories much faster than the ePlayer could and it has a number of specific visualization options Maestro can also perform basic quality analysis using the Simulation Quality Analysis panel and detailed geometric and energetic analysis of the trajectory can be carried out using the Simulation Event Analysis tool The following sections cover the basics of these tools Animating Desmond Trajectories with the Trajectory Player Assuming that you have completed the first exercise in this tutorial in Tutorial Steps on page 3 you should have a completed Desmond simulation of the 4pti structure in your working directory with the base name of desmond_job by default unless you gave it a different name 1 Select Project gt Import Structures Read in the desmond_job out cms file You will have to set the file format selector in the Import panel to Desmond to display Desmond cms files in the file browser window D E Shaw Research 87 Desmond Tutorial 2 Visualization and Analysis using Maestro Select Project gt Show
60. ase M2 Total Free Energy by FEP Prime f FEP Primex Simulation Quality Analysis QikProp Simulation Event Analysis QSite Metadynamics Analysis Semi Empirical SiteMap Strike Monitor Jobs This launches the Desmond System Builder panel shown in Figure 1 12 The System Builder generates a solvated system that includes the solute protein protein com plex protein ligand complex protein immersed in a membrane bilayer etc and the solvent water molecules with counter ions D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 12 Desmond System Builder panel April 2011 17 18 19 20 21 aE Solvation Ions Set Up Membrane Delete Membrane Solvent model None 7 a Select SPC ______l_ Predefined SPC x O Custom Browse Select Orthorombic eeano Box shape Orthorhombic r Box size raladas i Buffer Absolute size Select Buffer jie Set the distances to ne A Select Show boundary manne box O Custom Click Calculate Apply to Force field OPLS2005 x Start Write Reset i Close Help i Select SPC from the Predefined option menu Select Orthorombic from the Box shape option menu Select Buffer from Box size calculation method Enter 10 0 in the Distances box
61. ates var ious attributes such as name type mass charge etc This data is usually obtained from a structure file but missing values not supplied by the structure file are guessed and the stored values can be overridden using scripting commands as described below The snapshots associated with each molecule are referred to as frames Each frame holds one set of coordinates for each atom in the molecule as well as unit cell dimensions for that frame Velocities can also be stored if the trajectory file supplies them and the user requests it using the appropriate file type Table 7 1 summarizes the functions in the molecule module for querying the high level structure of molecules in VMD In the rest of this section we outline the Python interface provided by VMD to extract atom and frame information from a molecule D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Getting information about snapshots April 2011 Atom selections An atom selection consists of all the atoms in a particular molecule and frame that satisfy some predicate or set of conditions We often refer to the predicate as the selection but it should be kept in mind that the set of atoms satisfying the predicate could be different for different frames Atom selections are used in the GUI to select which atoms to draw with each style The same selection language is used in the scripting interface to specify a pred icate for an atom selecti
62. ations Host is usually a Linux cluster with dozens to hundreds of CPUs Click Start The Desmond simulation process begins execution Job progress appears in the Monitor panel similar to that shown in Figure 1 18 Figure 1 18 The Monitor panel Jobs 2 8 represent the relaxation phase 18 drdws0086 0 4d7a4b03 incorporated 2011 03 4pti_desmond_setup finished 0 11 17 07 d drdws0086 0 4d7bc9a5 4pti_Desmond_md_job incorporated finished 0 2011 03 12 14 29 41 d a A see di drdws0086 0 4d7bca66 4pti_Desmond_md_job_3 completed finished 0 d drdws0086 0 4d7bcacb 4pti_Desmond_md_job_4 completed finished 0 d drdws0086 0 4d7bcbc9 4pti_Desmond_md_job_5 completed finished 2 d drdws0086 0 4d7bcc92 4pti_Desmond_md_job_7 completed finished 2 d drdws0086 0 4d7bcd57 4pti Desmond md job 8 completed finished 0 d arawsvuso u 40 0ce 4 4ptl_vesmond_mg_joo comp teteu Tinisned u Z01L1 UJ 1Z 14 9V0i1Z d 4 Ty Show Jobs from Monitor Pause Details File Molecular dynamics Job launching command SCHRODINGER utilities multisim PROJ u nyc kolossva Playground build16 Desmond_Tutorial 0 6 4pti DISP append JOBNAME 4pti_Desmond_md_job HOST localhost maxjob cpu 1 2 2 m 4pti_Desmond_md_job msj c 4pti_Desmond_md_job cfg description Molecular dynamics 4pti_Desmond_md_job cms mode umbrella o 4pti_Desmond_md_job out cms File u nyc ko
63. ations can run on your host Maximum simultaneous subjobs 4 queue at the same time Stat Cancel 5 Alternatively click Write A total of four files are written Two Maestro files my fep job_lig mae and my fep job_cmp mae The first file contains the original ligand and one or multiple mutants The second file con tains the receptor and the ligand structures Note that both files are regular Mae stro files with no force field information included at this point The only information about the FEP setup in these files is the definition of the attachment bond Two MultiSim command script files my fep job_solvent msj and my fep job_complex msj The first script defines a series of simulations involving the ligands in the solvent and the second script defines corresponding simulations involving the ligand receptor complexes Both msj scripts can be run from the command line as described in Running MultiSim jobs from the Command Line on page 58 Mutants do not need to be stoichiometric equivalents as in this example Atoms that have no match in the mutant or vice versa will be annihilated into or grown out of dummy atoms during the course of the FEP simulation in accordance with the double topology technique For more realistic simulations you will need to adjust the conformation of the mutant See Adjusting the Conformation of the Mutant on page 77 for details This tutorial does not go into
64. bound to a protein versus the same ligand bound to a mutated form of the same receptor with amino acid residue mutations applied to the protein With the other calculation the difference in free energy is computed for a protein versus a mutated protein without a ligand Only single point mutations can be applied in a single FEP calculation To consider multiple mutations you must run multiple FEP calculations However you can always setup multiple single point mutations in a single FEP run for example to compare the effect on binding free energy of different single point mutations Ring atom mutation can be used to replace one atom with another in a ring structure Absolute or total free energy calculation can be used to compute absolute solvation free energies by annihilating a whole solute molecule 81 Desmond Tutorial 82 Preparing Free Energy Perturbation and Metadynamics Setup for these types of mutations is straightforward and very similar to ligand muta tion setup Please consult Chapter 4 and Appendix B of the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 for details about FEP setup and the syntax for programming msj scripts respectively Aside Metadynamics Metadynamics is a different kind of free energy perturbation method which enhances sampling of the underlying free energy space by biasing against previously visited val ues of user specified collective variables The biasing i
65. clicking 4 and next to HOH153 in the table you can flip through a pre defined set of discrete OH orientations and immediately view the result in the workspace Figure 1 10 shows the workspace when the water molecule is rotated out of the way Similarly residue states and OH orientations of other residues can be set manually and if desired locked by selecting Lock At this point we can confirm that the close contact has been eliminated Click View Problems in the Refine tab Figure 1 9 and you should see a popup window with the message There are no problems to report as shown in Figure 1 10 Finally by clicking Optimize you can further optimize the hydrogen bonding network via a computer algorithm For further information about the Interactive H bond Opti mizer click Help April 2011 D E Shaw Research 11 Desmond Tutorial NOTE NOTE Desmond Tutorial 15 Finally provided that you have a Glide license from Schr dinger the whole protein structure in the workspace can be subjected to constrained refinement by clicking Minimize in the Impref minimization subpanel on the Refine tab The preferred refinement procedure for MD simulations is to use Desmond s own mini mization relaxation protocol see below The Protein Preparation Wizard has two options to fill in missing side chains and resi dues via Prime provided that you have licensed Schr dinger s Prime application You only have to select the Fill in missing side chai
66. ct Auto Autto Retrieve from local installation Download from Web Click Download Download Enter the identifier for the PDB file you want to import into the PDB ID text box Select Auto to allow Maestro to download the PDB file from the PDB website Click Download The protein structure appears in the Maestro workspace as shown in Figure 1 5 The protein structure is displayed using a ribbon representation with colors continuously varying along the rainbow scale from the N terminus toward the C terminus The red dots show the location of the oxygen atoms of the water molecules present in the X ray structure D E Shaw Research 5 Desmond Tutorial Desmond Tutorial Figure 1 5 Imported protein structure file Click Ribbon and select Show Ribbons then select Delete Ribbons to switch to a different view Your protein appears lt in the workspace Red dots represent crystal water oxygen atoms Ribbon j e x Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help se Be E g RP Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz ml ay X KH eS NS h d GH 5 Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene A fice 2 o o D gt Wire CPK Ball amp Stick Tube Thin Tube Color
67. e RMSD relative to frame 0 pro0 atomsel protein frame 0 m prol0 fit pro0 weight mass prol10 move m D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Getting information about snapshots rms prol0 fit pro0 Snapshots Time varying data in VMD includes positions velocities and periodic cell parameters The atom selection interface can be used to extract positions and velocities from a given frame in the same way as other attributes get the x y and z coordinates for the atoms in wat1 as Python lists watl get x watl get y watl get z get the z component of the velocity vz watl get vz NK MM FH However this method comes with significant overhead if a large number of snapshots are to be processed and the Python lists returned by the get are not as efficient or conve nient to work with as NumPy arrays For this reason VMD implements a built in module called vmdnumpy that returns posi tions and velocities as NumPy arrays rather than lists The syntax is vmdnumpy positions molid 1 frame 1 Return reference to coordinates vmdnumpy velocities molid 1 frame 1 Return reference to velocities The arrays returned by positions and velocities are zero copy references to the snapshot data stored in VMD They will be sized as N x 3 arrays where N is the num ber of atoms in the molecule The x y and z components of the position or velocity are st
68. e Structures Molefacture Mutate Residue Nanotube Builder Parameterization Tool ID T A D F Molecule Atoms Loop stepaj 1 H speed The general workflow of setting up a molecular system for Desmond simulation in VMD is as follows 1 Load a molecule from any source that VMD can read for example load a protein structure from a PDB file 2 Use the modeling tools in VMD shown in Figure 7 7 to generate the simulation sys tem The tools provide similar functionality to that of the Protein Preparation Wizard and the Desmond System Builder in Maestro see Figure 1 6 on page 7 and Figure 2 2 on page 22 The main building tool in VMD is the popular Automatic PSF Builder 3 When you are satisfied with your setup save the system in a Maestro file Make sure that your system is selected in the VMD Main window click on it if it isn t highlighted in yellow and export a Maestro file by selecting File gt Save Coordinates and choos ing the mae file type 4 Use Viparr and the build_constraints script as described in Finishing Prepara tions for Desmond Simulation on page 47 to add force field parameters and con straints to complete the setup for running a Desmond simulation with a molecular system generated in VMD As an exercise try building a simulation system with the 4pti structure that we used in Desmond Tutorial on page 1 to introduce Desmond setup in Maestro Building a solvated protein system for Desmond simulatio
69. e attribute in the usual Python way nl len wat0 number of atoms in the selection f wat0 frame returns 1 wat0 frame 20 makes wat0 reference frame 20 n2 len wat0 will be equal to n1 wat0 update recompute the selection based on frame 20 n3 len wat0 might be different from nl Note however that changing the frame does not cause the selection to be recomputed Only the update method changes the set of atoms referenced by an existing selection However changing the frame does change the result of calculations that depend on the coordinates such as center and rmsd The reason things are done this way is because one might want to select a set of atoms based ona distance criterion such as the wat0 selection in the example above and then see howthe positions of those atoms change over time There would be no way to do this if changing the frame automatically updated the selection With an atom selection object in hand you can extract data about a molecule for the atoms in the selection Continuing from the first example Get the number of alpha carbons num_ca len ca get the residue name of each alpha carbon resnames ca get resname Set the type attribute of all atoms to X all set type X Compute the center of mass the protein atoms in frame 10 mass prol0 get mass com prol0 center mass Align prol0 to the corresponding atoms in frame 0 and compute th
70. e the box volume Besides the shape the box size also depends on how you define the solvent buffer around the solute e Apply a buffer distance to each dimension of the simulation box A typical buffer dis tance is 10 A which is equal to the usual real space Coulombic interaction cutoff for long range electrostatic calculations e Or set the absolute size of the box Next by clicking Minimize Volume you can instruct the System Builder to minimize the box volume by aligning the principal axes of the solute with the xyz or diagonal vectors of the simulation box essentially you can align the protein structure so that it fits inside its simulation box more comfortably However this method is only recommended if the sol ute is not allowed to rotate during MD simulation Selecting Show boundary box displays a helpful translucent graphical representation of the simulation box in the workspace System Builder puts the center of gravity of the solute at the center of the simulation box As a consequence fairly non spherical proteins will appear to shift toward one side of the box leaving only a thin water buffer on that side This may not be ideal from a visual per spective but in terms of periodic boundary conditions this is perfectly adequate It is not the distance between the outer surface of the protein and the near face of the simulation box that matters rather it is the sum of two such distances with respect to the opposite sides
71. e the prepared structure file a ie ligands or 5 Assign force field parameters fio Configure DESMOND ora tors to the structure using Maestro simulation parameters H Fill in missing residues or Viparr and side chains l i Setup the membrane F Solvate the system B Distribute counter ions fii Relax minimize your system and J Maestro tasks run the Desmond simulation J DESMOND specific tasks fiz Analyze results The rest of this section contains step by step procedures for building and running a simu lation of a single protein Tutorial Steps 1 Start Maestro from your Linux desktop by issuing the following command SSCHRODINGER maestro If you access Maestro through the network e g via VNC start the program by the command SSCHRODINGER maestro SGL This command will launch Maestro using a software OpenGL graphics library The Maestro environment appears as shown in Figure 1 2 If you are unfamiliar with Maestro the Schrodinger Suite or Academic Maestro distributions contain a Maestro Tutorial and User Manual that can be consulted for more detailed information April 2011 D E Shaw Research 3 Desmond Tutorial Desmond Tutorial Figure 1 2 Maestro main environment Select Project gt Import SB ETT x St t Project Edit View Workspace Tools Applications Workflows Scripts Window Help ructures a oS Fa H5 J PDB XS o a amp f me og Open SaveAs
72. eady present in the OPM Orientations of Proteins in Membranes database at the University of Michigan Using the System Builder you can import OPM placements as well as other pre aligned placements In this section we will import the OPM placement for 1su4 To import a membrane placement from the OPM database 1 Search the OPM database by typing 1su4 in the Search OPM box as shown in Figure 2 18 Figure 2 18 The OPM Home page April 2011 HOME ABOUT OPM DOWNLOAD OPM FILES CONTACT US LIPID COMPOSITION ATLAS _ Protein Classification Orientations of Proteins in Membranes OPM database Types 4 types OPM provides spatial arrangements of membrane proteins with Classes 11 classes Superfamilies 226 superfamilies Families 330 families Species 319 species Localization 22 types Each protein is positioned in a hydrophobic slab of adjustable bd Orientations of Proteins in Membranes OPM database Mozilla Firefox 5 I x File Edit View History Bookmarks Tools Help z http opm phar umich edu gt iG a fj Most Visitedy 6 CentOS Support UNIVERSITY OF MICHIGAN COLLEGE OF PHARMACY MOSBERG LAB ie OPM te membranes respect to the hydrocarbon core of the lipid bilayer OPM includes all unique experimental structures of transmembrane proteins and some peripheral proteins and membrane active peptides Features thickness b
73. ected atoms Coordinates File type Load State iv Save State I o Frames First Last Stride b jf h Save all at once K j zoom oop z step ft H pee DI Save in background Process the Maestro file with Viparr and the build_constraints script from the command line to add force field parametars and constraints Now you are ready to run a Desmond simulation You can either import the simulation system into the Des mond Molecular Dynamics panel in Maestro or you can run a Desmond simulation from the command line with this file and an appropriate Desmond configuration file as described in Running a Desmond simulation on page 56 D E Shaw Research 103 Desmond Tutorial 104 System Setup and Trajectory Analysis Using VMD Loading files from the scripting interface Files can also be loaded into VMD using the Tcl or Python scripting interface We ll con fine ourselves here to the Python interface although you may find using the Tcl interface with VMD TkCon window more convenient for simple tasks Type the command gopython in the VMD text window to start the Python interface Load the molecule module by typing import molecule at the Python prompt gt gt gt To load a structure file and all frames of a trajectory file henceforth we use the short hand trajectory dtr as the generic name of a trajectory file instead of trajectory_subdir clickme dtr enter the following commands import m
74. ed in better binding otherwise if ddG_binding is positive the original ligand molecule had more favorable binding Using Maestro To Generate A Desmond FEP Configuration File To create a Desmond conguration file for FEP 1 Select Applications gt Desmond gt FEP The FEP panel appears as shown in Figure 5 7 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Using Maestro To Generate A Desmond FEP Configuration Figure 5 7 Setting FEP parameters from the FEP panel Select the windows that should be included in the simulation by clicking the corresponding column head Click Write 2 LLL m Model system Load from Workspace v Load The system is not specified Simulation FEP type Mutation Total free energy Number of windows 12 1 Set lambda values automatically iam cml Vim ml Mma il Umi mc cl Vm Zam Lm imal Cid Lm Sul eae Vdwa lambda 1 1 1 1 1 0 674 0 4563 0 325 0 247 0 189 0 118 VdwB lambda 0 0 118 0 189 0 247 0 325 0 4563 0 674 1 1 1 1 1 ChargeA Lambda 1 0 75 0 5 0 25 0 o o o o o o o ChargeB Lambda 0 o o o o o o o 0 25 0 5 0 75 1 BondedA lambda 1 0 909 0 818 0 727 0 636 0 545 0 454 0 363 0 272 0 181 0 090 0 BondedB lambda 0 0 090 0 181 0 272 0 363 0 454 0 545 0 636 0 727 0 818 0 909 1 __ Use lambda hopping to enhance sampling Simulation time ns total 1 2 ela
75. eececeeseeneneeees 103 Figure 7 11 Saving the 4pti system in Maestro format cee ee eeeeeees 103 Figure 7 12 Analysis script example cc ccc cece cecseseeeeeececeeeesseseseseeeneneseeaees 109 D E Shaw Research April 2011 April 2011 Desmond Tutorial Introducing Desmond Desmond is an advanced classical molecular dynamics simulation system which has an intuitive graphical user interface integrated in the Maestro molecular modeling environ ment Using Desmond you can perform in silico simulations of small molecules proteins nucleic acids and membrane systems to study the interactions of complex molecular assemblies With Desmond you can generate high quality simulation trajectories of long time scales as well as compute a variety of thermodynamic quantities Desmond trajecto ries can be visualized and analyzed using numerous tools in Maestro and VMD This tutorial assumes a basic knowledge of molecular mechanics and molecular dynam ics For those users who have not yet used Maestro for molecular modeling an overview of the Maestro environment is included Beyond basic molecular modeling there are a number of steps that must be performed on a structure to make it viable for simulation with Desmond Each of these steps mandates an understanding of certain concepts and differing approaches that can be taken To enable novices and advanced users alike to process the information in this tutorial the organization of the tutor
76. ein Preparation Wizard Interactive H bond optimizer 0 10 Figure 1 10 Protein Preparation Wizard Interactive H bond optimizer 11 Figure 1 11 Launching Desmond System Builder cece ceeeeeeeeeteneeeeeees 12 Figure 1 12 Desmond System Builder panel cccccccsesec cee ee cesses eeseesseeseeseeeeees 13 Figure 1 13 Solute and boundary box in the Maestro workspace cccseseseeteseeeeees 14 Figure 1 14 Ions tab in Desmond System Builder c cece eee ceeeeeeceeeeeneeseees 15 Figure 1 15 Solvated protein structure in the workspace oo cece cents teeeeeees 16 Figure 1 16 The Molecular Dynamics panel ss ssessessessssssesessresesssesiestessssrestentesressesses 17 Figure 1 17 The Molecular Dynamics Start dialog DOX ccceceesssseesesteteteeceteeeseseenenenes 17 Figure 1 18 The Monitor pannel ccc ccc aE ER a 18 Figure 1 19 List of files in the Monitor panel ssssssssesssssssssessesssssesssssestessessnssenrenreesesses 19 Figure 2 1 Launching Desmond System Builder 0 0 ccc ec eeeeeeeeseeneceeeeees 21 Figure 2 2 System Builder panel sienna sonaye nir srie i aiii iaaa ep 22 Figure 2 3 Ions tab in Desmond System Builderpanel s sssssssssssssssssstessssssessseestesseeee 24 Figure 2 4 Membrane setup in the System Builder 0 0 0 ccccesseseseseeseseeseneesesesneeneeeeees 26 Figure 2 5 Preprocessing the 1su4 structure ssssssssessesssessestestsstertestesteserss
77. embrane protein system for Desmond simulation 1 Open the Protein Preparation Wizard by selecting Workflows gt Protein Preparation Wizard Type 1su4 in the PDB box and click Import as shown in Figure 2 5 When the structure appears in the Maestro workspace set the preprocessing options as shown in Figure 2 5 do not delete the crystal waters as they are integral to the protein structure Click Preprocess The tables will be filled in by the Protein Prepa ration Wizard Click the Review and Modify tab select the sodium ion in the Het table the focus of the workspace view will center and zoom on the Na ion and then click Delete The sodium ion is an artifact of the crystallization process only the Ca ions are integral parts of the protein You may want to experiment with H bond assignment as described in Figure 1 10 but it is not essential for the current membrane setup exercise Click Close to exit from the Protein Preparation Wizard panel D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Figure 2 5 Preprocessing the 1su4 structure Enter 1su4 in the PDB box and click Import Next check options in this section as shown Do not delete the crystal waters Then click Preprocess Setting Up Membrane Systems b 4 Protein Preparation Wizard Job prefix prepwiza rd Display hydrogens ONone Polar only All Import and Process
78. en completed there are a number of post processing options listed under Data Analysis that can be performed For example click Export Results to export results for further analysis in external spreadsheet programs In this example a number of quantities will be monitored along the trajectory including the total energy and torsional energy of the 4pti protein molecule and the RMS fluctua tion of the C alpha atoms Trajectory analysis and sophisticated visualization and analysis tools can be applied to Desmond trajectories utilizing the VMD visualization package which is covered in the next section D E Shaw Research 93 Desmond Tutorial Visualization and Analysis using Maestro This page left intentionally blank 94 D E Shaw Research April 2011 7 System Setup and Trajectory Analysis Using VMD April 2011 Overview VMD is primarily a molecular visualization program but it is a natural environment for analysis with its strong support for atom selections the ability to efficiently animate tra jectories that contain thousands of snapshots and support for Tcl and Python scripting languages The current release version of VMD 1 9 as well as 1 8 7 available at the VMD website http www ks uiuc edu Research vmd has the built in capability of writing Maestro files and reading Desmond trajectory files The former is useful for preparing your simulation system in VMD for running Desmond simulations and the latter allows for using
79. ent from the OPM Database Figure 2 22 Set Up Membrane dialog box bhg System Builder Set Up Membrane Membrane model Predefined POPC 300K v Custom Transmembrane atoms ASL optional Click Place on Prealigned Structure Select Set to Helices Place Automatically Adjust membrane position Place membrane perpendicular to the z axis of the structure in the Workspace with surfaces at Z and Z Save Membrane Position Load Membrane Position ok X cancel 3 Help The imported membrane placement is displayed in Figure 2 23 Figure 2 23 OPM pre aligned membrane shown in the workspace i Seen 77777 D NE Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help ma Gs ex GH gt PDB yg na Open Save As Import Export Table 2D Viewer Lig int GetPDB Prep Wiz Ft Fog Enhance Rotate X Rotate Y Tile amp r n H o X KR H oF MH Es a b Sele t Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image New Scene mb X X E A s e 0 00 9 9 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X xy y X X X X Y Find Atom number X N 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 1 353 15792 Entries S 1 2 Res 1114 Chn 3 Mol 121 Chg 27 Jobs 0 0 f middle xy rotate ctrl middle z rotate right xy translate
80. eparing Free Energy Perturbation and Metadynamics Figure 5 3 Ligand Functional Group Mutation by FEP panel fod sand Functional Group Mutation by FE ES Define Perturbation Plan Calculation 1 ini Select Pick the i Step 1 Display the ligand and its receptor if any in the Workspace attachment bond Pick the attachment bond to define the core and the Step 2 substitution group place the substitution group Step 3 Fragment library 9 items 1 item selected lali Fragment name view Reset Select the fragment that 2 netnyt Reset will replace the M PREN 2 ethyl Reset substitution group m 3 hydroxy Reset fa amino Reset I 5 ammonio _Reset Ma 6 carboxy Reset ET a 7 fluoro Reset 8 chloro _ Reset o hydro Reset O Desmond Click Start __ aes Research Start Write Reset 2 Select Pick the attachment bond Step 2 in Figure 5 3 Close Help When you define a structural perturbation for FEP the ligand molecule is separated into two parts a fixed part called the core and a variable part called the substitution group The substitution group will be mutated during simulation and the core will remain intact As shown in Figure 5 4 the core and the substitution groups are con nected by a single bond termed the attachment bond green arrow which has to be picked by hand Currently the attachment bond can only be a si
81. er but results will be more reliable For this exercise let s make a larger mutation in the ligand molecule and turn the whole NH CH CH NH side chain into a buty1 group The current view of the workspace should be similar to that shown in Figure 5 4 on page 65 1 Click Pick the attachment bond in the Ligand Functional Group Mutation by FEP panel see Figure 5 3 on page 64 and click OK when asked to confirm that you are reselecting the bond This time choose the attachment bond shown in Figure 5 8 For clarity the view is changed to wire frame representation D E Shaw Research 71 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 8 Picking the attachment bond for creating a butyl side chain Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help a EA A Fe 7 Fr a PDB yg Ba 38 Li id Ww a z3 kas v Y es gt Q A 3s ole Open Save As Import Export Table 2D Viewer Lig Int GetPDB PrepWiz Ft Fog Enhance RotateX Rotate Y Tile A Lal M A X KH GH MH BE a Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image New Scene wi Y X X 4 os S e ce 2 O0 O aD gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color les Gi gia 2 Sik A 7 R i A os Lis al oF L C 6 b SNA Draw SetElement Bond Order Bond Order FormalChg FormalChg Move R S Cleanup Sculpt Find
82. etPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile Open SaveAs impo A Lal ie KH go A Es a b Select Undo Redd Bketcher Add H Transform Adjust Create Entry Clear Save Image New Scene A p 08 oOo o gt gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color voy zo y YX Find Residue number y 219 N P 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 1898 9569 Entries 1 L Res 2003 Chn 4 Mol 1899 Chg 27 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 5 Delete the dummy atoms by clicking and holding the red X icon in the Workspace toolbar and launching the Selection panel In the Selection panel click the Molecule tab 7 Select Molecule type in the left panel and then DUM in the right panel as shown in Figure 2 21 April 2011 D E Shaw Research 41 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 21 Selecting the dummy atoms for deletion 42 NOTE NOTE v SEES ese F x Select To Delete Atom Residue Molecule Chain Entry Substructure Set Select DUM Molecule number Molecule type Molecule number in entry CA 2 Ci YC Molecular weight Piima datoms O A Select Molecule Size number of atoms
83. f systems simulated in adjacent lambda windows are attempted periodically For mutations involv ing conformational flexibility lambda hopping can improve convergence For details see April 2011 D E Shaw Research 67 Desmond Tutorial 68 NOTE Preparing Free Energy Perturbation and Metadynamics the the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 All of these options use the Schrodinger OPLS AA force field server Of course you can use Viparr to generate force field parameters for other force fields however Viparr has limited coverage of the chemical space of organic compounds which means that for most ligand mutations OPLS AA is currently the only viable force field 1 Compute the binding free energy difference between two different ligand mole cules Regardless of which method was used in step 6 two output mae files have been generated jobname_solvent out mae and jobname_complex out mae The dif ference in free energy between the ligand molecules in pure solvent 4G_solvent and the difference when bound to the receptor 4G_complex are recorded respec tively in these out mae files Import the mae files into Maestro open the Project Table and locate the dG values at the far end of the table The relative binding free energy of ddG_binding is equal to the difference between dG_complex and dG_solvent dG_complex dG_solvent If ddG_binding is negative the mutation result
84. for the OPM placed 1su4 system in Importing Membrane Place ment from the OPM Database on page 39 SSCHRODINGER run FROM mmshare relax_membrane py t 300 i 1su4_opm_Desmond_setup out cms You can directly import the resulting relax msj file as a suitable custom protocol in the Molecular Dynamics panel but you can also manually edit the multisim script beforehand to modify or introduce additional relaxation stages D E Shaw Research April 2011 Finishing Preparations for Desmond Simulation Specifying Desmond Simulation Parameters When you click Advanced Options the Advanced Options dialog box appears as shown in Figure 3 2 Options in the Integration tab for the MD task include the multiple time step RESPA schedule and constraints Some parameters are interdependent for example spinboxes for setting the time step schedule If you set the innermost time step and hit Return the midrange and longrange time steps are adjusted automatically Of course you can always manually edit the values or use the spinbox up down arrows to adjust the values Figure 3 2 Advanced Options for simulation jobs Controls output files Parameters for non for simulations bonded interactions Other parameters Parameters for such as those setting harmonic defining atom Thermostat and restraints groups barostat parameters Multiple time step _ VENTEN ENN parameters xN Integration Ensemble Interaction
85. he Maestro Trajectory Player in Figure 6 2 on page 89 Figure 7 4 VMD Trajectory Player 98 ID T A D F Molecule Atoms Frames Vol D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Loading and Viewing Trajectories The trajectory movie can be seen in the VMD OpenGL Display window shown in Figure 9 5 Note that VMD can handle much larger trajectories than Maestro Figure 7 5 VMD OpenGL Display VMD provides a number of trajectory analysis tools available from the Extensions gt Analysis menu in the Main window shown in Figure 7 6 Figure 7 6 VMD Analysis tools File Molecule Graphics Display Mouse ID T A D F Molecule BioCoRE Contact Map Data Multiseq Modeling gt NAMD Energy Simulation NAMD Plot BIR Spectral Density Calculator Ramachandran Plot RMSD Calculator RMSD Trajectory Tool Hydrogen Bonds Salt Bridges Sequence Viewer Timeline Truncate Trajectory VolMap Tool You can also setup simulation systems in VMD using tools from the Extensions gt Modeling menu Figure 7 7 April 2011 D E Shaw Research 99 Desmond Tutorial System Setup and Trajectory Analysis Using VMD Figure 7 7 VMD Modeling tools File Molecule Graphics Display Mouse Scheyens Analysis f BioCoRE gt Data gt Add lons Simulation Add Solvation Box Visualization Automatic PSF Builder Tk Console CG Builder I D Dowser Inorganic Builder Membrane Builder Merg
86. hin Tube Color Scheme Color Kaai X X X X Y N P 0 of 0 Click Ribbon and select Show Ribbons for All Residues from the option menu esidue number y 219 Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Workflows Scripts Window Help HO a Q Q A ale Ft Fog Enhance Rotate X RotateY Tilg d 5 Create Entry Clear Save Image New Scene Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 359 15797 6 15U4 A Entries 1 13 Res 1115 Chn 1 Mol 116 Chg 23 ii Jobs 0 0 BFISUIA X Pick atom to delete 6 Launch the System Builder by selecting Applications gt Desmond gt System Builder 28 and click the lons tab The panel appears as shown in Figure 2 7 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Setting Up Membrane Systems Figure 2 7 The lons tab in the System Builder panel NETE 0 Solvation lons Excluded region Exclude ion and salt placement within 7 o Aof Click Select _ _ SS a lon placement ONone Neutralize by adding 23 Na ions Recalculate Oadd I Na ions Advanced ion placement x Add salt Salt concentration 0 15 M Salt positive ion Na Salt negative ion c Force field
87. ial includes e Astep by step example that describes at a high level how to perform a simulation on a simple protein e In depth concept sections that cover the detailed information users will need in order to perform a simulation similar to our example This tutorial also includes conceptual information and steps for performing free energy perturbation FEP calculations FEP is useful for performing alchemical ligand muta tions to determine relative binding free energy differences which is a crucial task for such applications as computational drug design Moreover Desmond FEP can be used to com pute the absolute solvation free energy of a large variety of solutes as well as the change in free energy associated with protein residue mutation Another addition to this version of Desmond is improved support for metadynamics simulation setup and analysis D E Shaw Research 1 Desmond Tutorial Desmond Tutorial Steps to Perform Simulation on a Simple Pro tein While the example described in this tutorial is a basic simulation on a single protein the exercise is useful for learning the Maestro Desmond environment as well as in general investigating the molecular properties of different proteins Preparing a molecular model for simulation involves these general steps 1 2 9 Import a structure file into Maestro Prepare the structure file for simulation During this step you remove ions and mol ecules which are
88. ides several built in modules for loading data into VMD as well as querying and modifying VMD state The most important of these are the molecule module the atomsel module and the vmdnumpy module Use the built in help command to get the most up to date documentation for these modules Loading and Viewing Trajectories Thanks to its file plugin architecture VMD can load many different kinds of files To simplify the discussion we re going to assume that you re working with only two kinds of files e Structure files mae or cms files created by Maestro or Desmond These contain topology mass charge and possibly force field information about a single molecular system including any solvent or ions that might be present They also contain a sin gle snapshot of the positions of the atoms and of any virtual sites in that system and optional velocities You can read either of these files with VMD selecting the Maestro file type mae e Trajectory files dtr files created by Desmond Although we will always refer to a trajectory as a file the on disk representation of a dtr is in fact a directory containing metadata files as well as frame files holding the actual snapshots Resist the tempta tion to think of the frame files as being somehow independent of the rest of trajec tory they are not and renaming or moving them around will cause issues There are two file types in VMD associated with Desmond trajectories The default dtr
89. igure 2 20 Importing the OPM PDB file in the workspace 0 0 cece eee 41 Figure 2 21 Selecting the dummy atoms for deletion c ccc cesses eens eeeeees 42 D E Shaw Research vii Desmond Tutorial viii Figure 2 22 Set Up Membrane dialog BOX o ccccccceeccccccsesesescecsesesesescscssseseececsesnenseeesees 43 Figure 2 23 OPM pre aligned membrane shown in the workspace ccceeeees 43 Figure 2 24 Full membrane simulation system for 18U4 ssssssssssssssesssssertssrerressesseeee 44 Figure 2 25 OPM transmembrane hole in the POPC bilayer for 1su4 oo 45 Figure 3 1 Setting up a Desmond simulation ccccccsseeseseeteteeceeetesceceteneneseeeeeseeeeeenes 52 Figure 3 2 Advanced Options for simulation jobs ccscsesesceeesesesesteneesesesneneeeeeenes 53 Figure 4 1 Running a Desmond simulation 0 0 0 ccc ceeee cece ceeeeseececenenetenenenenes 56 Figure 5 1 FEP Example Ligand mutation esceseeeeeeceseesneeesesensneneeeeeses 62 Figure 5 2 The ZINC 01538934 ligand Structure cccssceseesescenstesesesneteteseeceenesssnenenes 63 Figure 5 3 Ligand Functional Group Mutation by FEP panel ccceceereeenenes 64 Figure 5 4 Defining the mutation 00 0 0 ccs cscesesesesceeseseecscseseseseecscssseseeseseseneseeeesses 65 Figure 5 5 Ligand Functional Group Mutation by FEP Start dialog box 00 66 Figure 5 6 FEP workflow Control sirosis sssecs cesses cececesseseececensnsnseececessnsnesesenenssesese
90. into the same molecule For example vmd m mae moll mae mol2 mae f mol3 mae dtr trajectory_subdir clickme dtr In this example three molecules will be created The first molecule will take data from moli mae the second will take data from mol2 mae and the third will take data from both mol3 mae and the trajectory file referred to by trajectory_subdir clickme dtr Think of m for loading multiple molecules while f is for loading multi ple files Note that the command line loads all the snapshots from all the specified files before giv ing control back to the user If your trajectories are so large that not all snapshots will fit into memory you ll need to use either the graphical user interface or the scripting inter face to load a subset of snapshots into memory instead Loading Files from the GUI VMD s File menu lets you load cms and dtr files using a graphical user interface GUI Select File gt New Molecule in the Main menu Figure 7 1 Click Browse navigate to your structure file and click OK or press Enter to select the file You should now see your file in the Filename field and underneath the filename the file type chooser should show Maestro File as its selected item Figure 7 2 When the file and its type are to your satisfaction click Load to proceed Figure 7 1 Loading files from the GUI Select File gt New Atoms Frames Vol Molecule Load State Save State Once you ve loaded a
91. ion found in the HELIX section of the 1su4 PDB file If such information is not present in your PDB file try Tools gt Assign Secondary Structure in Maestro As you will see however this place ment will not be satisfactory in this case By specifying the set of transmembrane atoms more accurately you can expect a highly improved auto placement 7 Selection of transmembrane residues can be done a number of different ways using the Select panel In this tutorial exercise let s assume that we do not know the rele vant residue numbers that we could simply add in as an ASL expression and try to make an approximate selection by hand In order to do this change the Select tool in the Edit toolbar circled in Figure 2 12 to R residue selection and select a rectan gular area with the cursor around the transmembrane helices of 1su4 as shown in Figure 2 12 32 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Setting Up Membrane Systems Figure 2 12 Selecting transmembrane residues April 2011 Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help a U wham KF FETS A amp a Save As Import Export Table 2D Viewer Lig Int GetPDB PrepWiz Ft Fog Enhance Rotate X Rotate Y Tile A xX AHO MA amp E G indo Redo Delete Sketcher Add Transform Adjust Create Entry Clear Save Image New Scene e C re Oo F gt pa Ribbon Wire CPK Ball amp Stic
92. iple structures v Import associated data files For SD file eate ti For PDB files read alternate locations SD molecule name Open Protein Preparation Wizard after importing PDB file D propert 5 oe File name 4pti pdb Open Select PDB from the Files Files of type PDB pdb ent X cancel of type option menu A 4 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Click Options Set options as desired for the import Default settings are usually ade quate Click Help to learn about specifics of different options Choose PDB from the Files of type option menu Navigate to and select the structure file you will import and click Open For this example we will import the small proteinase trypsin inhibitor protein 4pti Therefore the 4pti pdb file has been chosen NOTE Maestro supports many common file formats for structural input Click Help for a list of supported formats If you want to download the PDB file from the PDB website choose Project gt Get PDB The Get PDB File dialog box appears as shown in Figure 1 4 Figure 1 4 Get PDB File dialog box April 2011 lo Get PDB File ZZZ Enter the identifier for 5 3 PEE p Note Downloading will create the PDB file in the the PDB file you want to current directory and then automatically import it import in the PDB ID PDB ID 4pti i i text box Chain name optional Sele
93. k Tube Thin Tube Color Scheme Color ye a a 2 X X Y Find Residue number x 219 N P 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 6182 6182 15797 Entries 1 13 Res 1115 Chn 1 Mol 116 Chg 23 Jobs 0 0 te nce LPA F WELY FEDLL A ST j KALGIVATTGVSTE IGK NOMNAR ENEP ECCS AKKNA IVRSIM9SYTLGCTSV ICSDKTGTLTTNOMSVCKMF I IDKVDGDFCSLNEFSITGSTYAPEGEV 6 RERE A 6 ISU TK LKNDKP IRSGOFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVANLSKVERANACNSVIROLMKKEFTLEFSRDRKSH 2 6 ISU4 A SVYCSPAKSSRAAVGNKMF VKGAPEGV IDRCNYVRVGTTRVPMTGPVKEKILSV IKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSREMEYETDLTF a 6 ISU4_A VGVVGMLDPPRKEVMGS IQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLO middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu The selected residues will be highlighted in yellow color After making the selection in the workspace click Select in the Set Up Membrane dialog box to open the Atom Selection dialog box and click Selection as shown in Figure 2 13 D E Shaw Research 33 34 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 13 Importing the selection into the Atom Selection dialog box Stom seiection Define transmembrane atoms Atom Residue Molecule Chain Entry Sub
94. l 2011 Maestro 4pti pr 77 Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help TA 1 zee PDB o Ba aie e Uram Be FP FISTS A amp Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile fea Le oA 4 Ma x HESI amp Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene T X A sce o oo 6 9 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color a Meat E Mi i X X Y 7 219 n P 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Find Residue number Resulting simulation system for 1su4 mae protein shown as a CPK model for clarity aa Note that the wae protein is shifted toward the top of the simulation box Note the gaps between the water layers that are associated Lipid bilayer with the lipid shown in green bilayer and the added water buffer at the top and the bottom of the simulation box Atoms 0 146065 146065_ Entries 1 14 Res 35622 Chn 3 Mol 34648 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu D E Shaw Research 37 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 17 Transmembrane hole in the POPC bilayer for 1su4
95. lder and the msj command script file which defines the custom relaxation protocol The custom relaxed system will be saved in the lt jobname gt out cms file The msj syntax as well as a complete list of MultiSim options can be found in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 and the help option can be used for quick reference The MultiSim facility has a very useful restore mechanism If a MultiSim job fails for example an FEP job may involve hundreds of individual Desmond subjobs it can be restarted from a MultiSim checkpoint file so that only incomplete jobs crashed or not yet run will be re run The MultiSim msj file syntax provides an elegant and powerful alternative to Desmond cfg files The user can fully configure Desmond separately for each MultiSim stage inside the msj script itself The corresponding cfg files will be generated automatically for each subjob Also note that configuration settings in the msj file take precedence over settings in cfg file s D E Shaw Research 59 Desmond Tutorial Running Desmond Simulations This page left intentionally blank 60 D E Shaw Research April 2011 5 Preparing Free Energy Perturbation and Metadynamics Overview You can use Desmond to run free energy perturbation FEP calculations using the dual topology approach to perform ligand and amino acid residue mutation annihilation absolute free energy calculation
96. le se ai Bef rame000000001 the directory containing the frameo00000002 F clickme file frameoo0000003 frame000000004 frame000000005 frame000000006 frame000000007 M Preview Filename POTERS EA OK 7 Cancel At this point you may wish to limit the number of snapshots that are loaded from the trajectory In the Molecule File Browser Figure 7 2 the file type should automatically be reset to Desmond Trajectory and the Frames box underneath should now be active Type in values for the snapshots you want to load The default First value of 0 corresponds to the first snapshot in the trajectory the default Last value of 1 corresponds to the last snap shot and a Stride of 1 means load every snapshot in the selected range Choosing a Stride of 10 would load every 10th snapshot from the trajectory You also have the choice of Load in background which is slower but keeps VMD respon sive during the load and gives you the option of canceling the load before it completes and Load all at once which is quite a bit faster but leaves VMD in an unresponsive state until the load has completed Use Load all at once whenever you re reasonably sure that all the frames you re about to load will fit in memory After loading the frames you should see similar molecular information in the VMD Main window shown in Figure 7 4 At the bottom of the window you can see the controls of the VMD Trajectory Player quite similar to those of t
97. lecules neutralizing ions and counterions which serves as the input for system setup my_setup csb This is the command file which can be hand edited for custom setup cases For detailed documentation of the csb file see the Schr dinger Des mond User Manual listed in Documentation Resources on page 111 And a single output file besides a log file my_setup out cms This is the Maestro structure file of the entire membrane simulation system including OPLS AA force field parameters For detailed doc umentation of the cms file see the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Importing Membrane Placement from the OPM Database b Execute the following command at the command line SSCHRODINGER run S SCHRODINGER utilities system_builder my_setup csb where my_setup is the file name given to Write NOTE You can automatically perform setup of a GPCR membrane system by running this script from the command line SSCHRODINGER run mold_gpcr_membrane py Use the help option for usage mold_gpcr_membrane py takes an input GPCR structure in mae format and aligns it to a pre equilibrated protein membrane system from a list or a user defined template Importing Membrane Placement from the OPM Database In many cases you can find a high quality membrane placement alr
98. lee ee 1 Introducing Desmond Srii eia Diets e seer used oie ee Apne ane e ined te 1 Steps to Perform Simulation on a Simple Protein 2 2 0 2 000000 2 Tutorial Stepsis 4 3 has ie ase be ee ae ce ae SS eee ee hel be Lhd Bogs 3 2 Preparing a Desmond simulation with the System Builder 21 OVOCEVIEW E E ene eee ee E eet et ae eS ee ed eee eee 21 Selecting Solutes and Solvents 2 2 ee 22 Defining the Simulation Box 6 ee 22 System Builder Output File Format 2 0 0 0 0000000000000 23 Adding Custom Charges gct g sorea aea ee ee 23 Adding TOMS is e a e eoo a aean A Ta d sees Gh A A eR bo eed aa 24 Generating the Solvated System oaoa aa en 25 Setting Up Membrane Systems aaa ee 25 Importing Membrane Placement from the OPM Database 39 3 Finishing Preparations for Desmond Simulation 0000000 eee 47 OWVerVIEW rr oea ee aid lia a EA e Rh ee hase top Gola deed Jello vy kee ete wee Shai ee 4 47 Generating Force Field Parameters with Viparr 000 47 Adding Constraints sea gor bo eee a a ee a ee 51 Importing a Simulation System from the Amber Molecular Dynamics Package 51 April 2011 D E Shaw Research Desmond Tutorial Specifying Desmond Simulation Parameters 0 0 00 00 0000 51 Using Desmond applications in Maestro 000 51 Editing the Desmond Conguration File Directly 0 54 4 Running Desmond Simulations
99. lete Sketcher AddH Transform Adjust Create Entry Clear Save image New Scene The following problems were found with this structure Ribbon all amp Stick Tube Thin Tube Color Scheme Color Om ype Missing Atoms Overlapping Atoms A Residue number ECAN The following atom pairs are overlapping Atom 1 Atom 2 Distance 868 1060 0 514611 NOTE hydrogen overlaps can often be fixed by optimizing H bond assignment which can be do from the Refine tab of the main window Update Update the dialog tables based on the current Workspace structure JOK bed Bae The Display Hydrogens option in the Protein Preparation Wizard is set to Polar only in Figure 1 7 and therefore aliphatic hydrogens are not shown in Figure 1 8 Also note that the added capping groups can be seen in the circled area shown in wire frame representation 14 At this point you should have a topologically correct molecular system in the work space which can be subjected to molecular mechanics calculations However since hydrogen atoms were added by the Protein Preparation Wizard using simple geomet ric templates the hydrogen bond network should be optimized For example as shown in Figure 1 8 in this tutorial exercise the Protein Preparation Wizard reports a problem with atoms 868 and 1060 being too close see circled area Hydrogen atom 868 belongs to ARG53 and hydrogen atom 1060 belongs to HOH153 one of the crystallographic water molecules
100. library by selecting Edit gt Build gt Fragments The panel opens with the Fragments option menu set to Diverse Fragments as shown in Figure 5 11 Select Grow select Pick and select Bonds Then select the grow bond with the mouse as shown by the bright green arrow in Figure 5 12 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Creating a Custom Fragment Group Figure 5 11 The Build panel wv ETIC Select Grow Atom Residue Fragment Properties Properties Define grow bond Select Pick and select Pace l Grow sp pick Bonds Bonds Fragments Diverse Fragments Select an object to pick _ methyl ethyl propyl butyl pentyl isopropyl isobutyl isopenty tert butyl Diverse Fragments neopenty 3 3 dimethyibuty I cyclohexyl cyclohexyimethy 2 cyclohexylethy should be selected in the 3 cyclohexylpropyl 4 cyclohexylbutyl trifluoromethyl hydroxy hydroxymethyl Fragments option menu 2 hydroxyethyl I 3 hydroxypropy 4 hydroxybutyl I 5 hydroxypentyl I amino ammonio ammoniomethy 2 ammonioethy 3 ammoniopropy 4 ammoniobuty 5 ammoniopentyl I cyano II cyanomethyl 2 cyanoethyl 3 cyanopropyl 4 cyanobutyl 5 cyanopentyl morpholino I protonated morpholino morphlinomethyl protonated morphlinomethyl I 2 morpholinoethyl
101. lick Adjust to enable A mn 4A A G Ei FA Display Contacts L g D Draw SetElement Bond Order Bond Order Forma Rotate Peptide Plane Ceanup Sculpt Find Atom number N Rotate Carbonyl Plane Convert Cis Trans Project Edit View Workspace Style Saved Views Displ bels Build Fragments Distance Angle Dihedral Chirality Delete Adjustments Rotamers Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 2 Click the attachment bond shown in green to display the non bonded contacts between the buty1 fragment and the ligand core If you don t see any contacts shown in the workspace select Display Contacts in the Adjust tool and also make sure that the Quick Torsion option is set Click and hold the left mouse button to bring up the Adjust tool s option menu As shown in Figure 5 15 there are numerous allowed close contacts displayed in orange and a few unfavorable contacts displayed in red 78 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Adjusting the Conformation of the Mutant Figure 5 15 Displaying the non bonded contacts Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help m eel l FE 2 PDB yg wa a w om H g F T NnS A G Open Save As Import Expor
102. ll generate a smooth animation with your current display settings and you can even save it in an MPEG movie file for incorporation in any presentation material You can also save selected snapshots of the trajectory in Maestro format Options to center the trajectory view in the Trajectory Player include Center molecules in the Display section of the Trajectory panel under Positioning allows you to post process a trajectory such that the part of the system defined in the ASL text box will be centered in the simulation box This option is very useful when the solute appears to jump in and out of the primary simulation box which can be a visual artifact caused by the application of periodic boundary conditions The Center molecules option is a post processing option that only affects visualization and leaves the actual trajectory intact Note that the Center molecules option solves the same visual artifact issues during simulation that the Glue close solute molecules together option solves the Glue close solute molecules together option can be found in the Output tab of the Advanced Options dialog box for the Molecular Dynamics panel See Figure 3 2 on page 53 mdsim trajectory center is an option that can also be used to center the trajec tory in the simulation box this option can be set in the Desmond cfg configuration D E Shaw Research April 2011 Visualization and Analysis using Maestro Animating Desmond Trajectories with the Trajec
103. ll print all unmatched residues and exit with an error A maximum of 5 messages are printed per unmatched residue name e If any residue is matched by more than one of the selected force fields Viparr will print a warning message The user should be cautious and be responsible for any intended use of multiple force fields with multiple matches Besides the f option there are two more basic options The c option allows the user to assign parameters for a particular structure CT block in the input cms file and the n option provides a means to include a user defined comment in the output cms file for annotation purposes Viparr also supports user defined special force fields the d m and p options but that is beyond the scope of this tutorial Please refer to the Desmond User s Guide for information D E Shaw Research April 2011 Finishing Preparations for Desmond Simulation Adding Constraints April 2011 NOTE Adding Constraints While the System Builder automatically adds all the necessary constraints to the cms file Viparr does not If you process a mae or cms file with Viparr you will have to add the con straints in a separate step by running the following command SSCHRODINGER run FROM desmond build_constraints py input mae output mae where input mae is typically the Maestro file with Viparr parameters and output mae will include the constraints The command SCHRODINGER run FROM desmond build_constraint
104. lossva Playground build16 Desmond_Tutorial 0 6 4pti_Desmond_md_job_multisim log Multisim runs in the umbrella mode Booting the multisim workflow engine multisim version mmshare version Jobname Username Master job host Subjob host Job ID multisim script Structure input file CPUs per subjob Job start time Launch directory 3 8 3 36 20105 4pti_Desmond_md_job kolossva localhost localhost drdws0086 0 4d7bc9a5 4pti_Desmond_md_job msj 4pti_Desmond_md_job cms TERAS Sat Mar 12 14 30 09 2011 u nyc kolossva Playground build16 Desmond_Tutorial 0 6 SCHRODINGER d en klepeisj 2 SCHRODINGER suite2011_build16 Install_Academic Parsing the multisim script file Close Help Jj The job relaxation equilibration and the production run will finish in about an hour on 4 CPUs and at that point the Jobs tab in the Monitor panel will display a list similar to that shown in the upper part of Figure 1 18 If you run the job on a smaller number of CPUs you may want to shorten the simulation time accordingly Jobs numbered 2 8 represent the relaxation phase shown in the red rectangle of Figure 1 18 The first job in the list is the master job and the last job is the produc tion run There is an additional solvate pocket stage number 6 for systems that require special treatment for explicitly solvating a binding pocket which is not included in the standard System Builder setup By default
105. ls Build Fragments The butyl substitution group is shown in the workspace Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu Adjusting the Conformation of the Mutant The initial conformation of the mutant must be as close as possible to that of the original ligand for FEP simulations Using Maestro you can make manual adjustments to the con formation of small molecules 1 Click Maestro s Adjust tool as shown in Figure 5 14 to turn on the manual adjustment option Toggle this tool to switch between manual adjustment mode and global trans lation rotation mode April 2011 D E Shaw Research 77 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 14 Manual adjustment of the substitution group conformation Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help al Ba roo of yg Ba ae On 5 E EE ff ee Y es A sis Serort Table 2D Viewer Lig Int GetPDB_ Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile manual adjustments such z d 5 j amp y r 2 as quick torsion mode XA xX A H F l a a 6 Select Undo Redo Delete Sketcher Add H Transfor reate Entry Clear Save Image New Scene 2 Q A Q e E o Quick Torsion Ribbon Wire PK Ball amp Stick Tube Thin Tube Color ac Display H Bonds C
106. mics simulations It assumes a broad familiarity with the con cepts and techniques of molecular dynamics simulation and the use of the Maestro molec ular modeling environment Prerequisites April 2011 Desmond runs on Intel based Linux systems with Pentium 4 or more recent proces sors running CentOS 3 RHELS3 or later Linux clusters can be networked with either Ethernet or Infiniband Viparr requires a recent version of Python we recommend Version 2 5 1 This tutorial assumes that someone has prepared the Desmond Maestro environment for you either by installing the packages available from Schr dinger LLC or the Academic release of Desmond available from D E Shaw Research Where noted the procedures described in the tutorial make use of software that is not included in the Academic ver sion In those cases the software is available from Schr dinger D E Shaw Research i Desmond Tutorial About this Guide Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 This manual contains the following sections describes Desmond and outlines the steps to perform a simulation on a simple protein describes the System Builder the tool for setting up molecular systems for simulation using Desmond describes force field parameter assignment program Viparr and making changes to the configuration file output by the system builder describes how to run Desmond within the Maestro e
107. ming Simulation Event Analysis The Simulation Event Analysis tool SEA can be accessed from the Applications gt Desmond menu SEA is a sophisticated analysis tool described fully in Chapter 5 3 of the Schrodinger Desmond User Manual listed in Documentation Resources on page 111 Here we only intend to give a flavor of using SEA The Simulation Event Analysis panel is shown in Figure 6 6 When the SEA panel opens the Trajectory Player panel opens automatically and the Workspace view changes to only show the solute in wireframe representation Keep the Trajectory Player panel open for the full duration of the analysis Figure 6 6 Simulation Event Analyis panel 92 RA Simulstion event Anelys s NY Structure nd_md_job_long out cms Browse Import From Project Table Properties Data analysis Energy L H Bonds RMSD_ RMSE Measurements Double click to view or edit properties Time series ey 7 Time seres Ener roperties to monitor erg Svenee Energy_Total_Solute_Unnamed Histogram RMSF C alpha Unnamed Multi variable plot Lisoulome Statistics _ van der Waals Heat map Polar plot _ Bond RMSF plot Angle Auto select Torsion Multiple windows l Pick molecule for energy properties Multiple plots per window Multiple lines per plot Solvent display Hide solvent Show solvent within angstroms Show all solvent Remove Reset Analyze Analyze All
108. mpdir username jobname where tmpdir is specified in the s CHRODINGER schrodinger hosts file username is the username under which the job was submited jobname is the name of the Desmond job Use the LOCAL option to keep all job files in your working directory all the time Detailed documentation of several more options for running Desmond on the command line can be found in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 and the help option gives a quick reference with examples Although running Desmond from the command line as described in this section is fully functional the preferred way of running even single jobs is via the MultiSim utility Running MultiSim jobs from the Command Line It is often necessary to run multiple jobs either sequentially or simultaneously to com plete a particular computational task The two most common cases are system relaxation and FEP simulations System relaxation was discussed on Figure 1 16 on page 17 and FEP simulations are introduced in Preparing Free Energy Perturbation and Metady namics on page 61 Multiple jobs are handled by the MultiSim facility MultiSim reads a msj command script file and runs multiple simulations defined within it For instance to apply a cus tom relaxation protocol the following command can be used SSCHRODINGER utilities multisim JOBNAME lt jobname gt maxjob lt maxjob gt cpu lt cpu gt HOST localhos
109. mulation in the Molecular Dynamics panel As discussed earlier Desmond should perform structure relaxation to prepare a molecular system for production quality MD simulation Mae stro s built in relaxation protocol includes two stages of minimization restrained and unrestrained followed by four stages of short MD runs with gradually diminishing restraints and increasing temperature The relaxation parameters may also require edits The relaxation protocol is written to a msj command file multisim job which can be run from the command line see Running MultiSim jobs from the Command Line on page 58 You can manually adjust the relax ation parameters by hand editing the msj file If you decide to run the simulation from the Molecular Dynamics panel you will be limited to use the built in OPLS AA force field You can use Viparr to generate other than OPLS AA parameters but currently if you run the simulation using Viparr you will need to run it from the command line Running Simulations from the Molecular Dynamics Panel 1 Click Start at the bottom of the Molecular Dynamics panel to launch Desmond simula tion jobs directly from Maestro The Molecular Dynamics Start dialog box appears as shown in Figure 4 1 D E Shaw Research 55 Desmond Tutorial Running Desmond Simulations Figure 4 1 Running a Desmond simulation Sbisct Append hew ey moiecuiar dynamics Start THAD entries to add results to nuit the current
110. n 1 Load the 4pti protein structure from the PDB file in your working directory using the procedure depicted in Figure 7 1 on page 97 and Figure 7 2 on page 98 but using the pdb file type Alternatively start VMD from the command line with the vmd Apti command The structure should appear in the VMD Display window as shown in Figure 7 8 The protein structure will be displayed in a wire frame representation to show the structure as depicted in Figure 7 8 change the drawing method to lico rice in the Graphical Representations window for better picture quality 100 D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Loading and Viewing Trajectories Figure 7 8 Loading 4pti pdb into VMD 2 Select Extensions gt Modeling gt Automatic PSF Builder from the menu shown in Figure 7 7 The AutoPSF window appears as shown in Figure 7 9 Under Options select the Add solvation box and Add neutralizing ions options April 2011 D E Shaw Research 101 Desmond Tutorial System Setup and Trajectory Analysis Using VMD Figure 7 9 VMD AutoPSF window g Options Help Step 1 Input and Output Files Molecule 1 4pti pdb Output basename 4pti_autopsf Topology files proj desres root Linux x86_64 vmd 1 8 7a57 12 lib plug B Add 7 Delete Load input files Step 2 Selections to include in PSF PDB i Everything W Protein 4 Nucleic Acid J Other Guess and split chains using curren
111. n view for the remainder of this membrane setup exercise D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Setting Up Membrane Systems Figure 2 14 Initial automatic membrane placement for 1su4 v Maestro 4pti pr Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help oR BRUGES K F FOS A g B Open Save As Imnort Fynort Table IN Viewe GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile Rm X SX H S amp d amp Select Undo Redo Delete Sketcher Add Adjust Create Entry Clear Save Image New Scene Click Transformations to switch between local and global scopes t a D lcs 2 o Ribbon Wire PK Ball amp Stick Tube Thin Tube Color Scheme Color fp Tog Thin Tg g olog Click Ribbon and Residue RA 7 219 N P 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments select Show Ribbons from the option menu Initial automatic placement for 1su4 Atoms 5379 5379 15799 Entries S 1 13 Res 1116 Chn 2 Mol 117 Chg 23 Jobs 0 0 6 15U4 A XMERAHSKSUEECLASEGUEEMIGLID FS 6 1sUa A B ISUJ A RAVNODKENMLPSGTNIAAGKALGIVATTGVSTE IGK TRDOMAATE O RTVE CrISUT A SORA NEED Zee MENA TRAMAKKNA IVRSLPSVETLGCTSV ICSDKTGTLTINOMSVCKMF I IDKVDGDFCSLNEFSITGSTYAPEGEV 6 ISU4_A LKNDKP IRSGOFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK
112. nd a remaining net total charge D E Shaw Research 31 Desmond Tutorial Preparing a Desmond simulation with the System Builder d Import the resulting cms file back to Maestro and re run the System Builder with the appropriate solvent and the neutralize option with no further appli cation of the advanced ion placement procedure 5 After setting the Solvation and lons options click Setup Membrane in the Solvation tab of the System Builder The Membrane Setup dialog box appears as shown in Figure 2 11 Figure 2 11 Set Up Membrane dialog box 25 sem Bullder Set Up Membrane Aa Select POPC as the Trane model membrane model Predefinea POPC 300K v Custom Browse Transmembrane atoms ASL optional fres sec helix Select Se Click Place Place Automatically Place on Prealigned Structure Automatically Adjust membrane position Save Membrane Position Load Membrane Position ok X cancel SfHelp 6 Set the membrane model to POPC Other membrane models include DPPC and POPE The temperature in parentheses shows the temperature at which the mem brane model was equilibrated Note that even though the panel suggests it custom lipid models are currently not supported If at this point you click Set to Helices and then Place Automatically the System Builder will attempt to position the membrane bilayer at a reasonable location based on the informat
113. nen 67 Figure 5 7 Setting FEP parameters from the FEP panel ccc cscs cette eeeeeeees 69 Figure 5 8 Picking the attachment bond for creating a butyl side chain 0 72 Figure 5 9 Selecting the methyl group as the base for the butyl substitution group 73 Figure 5 10 The intermediate methyl substitution group shown in the workspace 74 Figure 5 11 The Build Rae EEE AEE EEEE Ted ck A E TR a 75 Figure 5 12 Selecting the grow bond ss ssusssssesssssssssssesstssessiesesseesensnentestesnnsnententeseesseseenee 76 Figure 5 13 The butyl substitution group shown in the workspace ss ss sssssssess111sse 77 Figure 5 14 Manual adjustment of the substitution group conformation 0 78 Figure 5 15 Displaying the non bonded contacts cccccesesssesseneeseseeteteseeceseenesesneneees 79 Figure 5 16 Unfavorable contacts removed cccccsessesssesesseteseeceeeseseeceneeneseseenessseeeenes 80 Figure 5 17 Butyl group superposed with original side chain 0 0 0 cece 81 Figure 5 18 Fragment library Build panel cccccccccccsesesescscseseseseecseseenseececsessenseeeeees 83 Figure 5 19 Metadynamiics panel i cssccsssesosersescgnesoedessorstunstotocdionstonecstenvennanisopseutoess seeeuasts 84 Figure 5 20 Metadynamics Analysis panel cccccessssesesessetesceceesessseeneeneseeeeesseeeeenes 85 Figure 6 1 Launching the Trajectory Player cece eseeeseeeetesseeeeneneteeseeees 88 Figure 6 2 The Trajector
114. ngle covalent bond in the molecule NOTE When selecting the attachment bond you determine the direction of the arrow by which half of the attachment bond you select The attachment bond arrow should point from the core to the substitution group 64 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Setting Up an FEP Calculation Figure 5 4 Defining the mutation Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help RbhDs ee EUS A TB Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Ft Fog Enhance RotateX Rotate Y Tile mn X KH NS amp FH 5 Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene scoe 6o00 6 8 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X y X X X X i e K wz Z R K sa e G s W ei Lok G b SN GF D Draw Set Element Bond Order Bond Order Formal Chg Formal Chg Move R S Cleanup Sculpt Find Atom number X e O of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments The attachment bond is shown as a green arrow in the workspace The arrow should point from the core to the substitution group 3 Define the mutation to be performed by selecting the fragment s that will replace the substitution group from the Fragment Library For this example select the meth
115. ns using Prime option or the Fill in missing loops using Prime option see Figure 1 7 Note that by selecting either of these options Prime will run with default settings Consult the Prime documentation for more advanced options including filling in loops in the presence of a membrane bilayer 16 The 4pti structure is now ready for preparing a Desmond simulation Select Applications gt Desmond gt System Builder as shown in Figure 1 11 Figure 1 11 Launching Desmond System Builder Select Applications gt Desmond gt System Builder 12 7 Maestro 4pti prj Window Help Maestro Project Edit View Workspace Tools Applications Workflows Scripts iss al fz Pd Task View Ba aje H wam E an l G aA Ge sis Open SaveAs Import Export Table 2D Viewer Lig O mpiciide Fit Fog Enhance Rotate X Rotate Y Tile F F ConfGen s KR H coreHopping gt aa 6 Select Undo Redo Delete Sketcher auu _ X Desmond System Builder E X 7 A Epik Minimization Joe 2 o Ribbon Wire CPK Ball amp Stick Tube ThinTube Color Slide 4 Simulated Annealing y y y yo y Find Specified atoms Select impact Molecular Dynamics Project Edit View Workspace Style Saved Views Dis Jaguar Replica Exchange Liaison Metadynamics LigPrep Ligand Functional Group Mutation by FEP MacroModel gt Protein Residue Mutation by FEP MCPRO hs Ring Atom Mutation by FEP Ph
116. nvironment and from the command line describes Free Energy Perturbation and metadynamics simulation using Maestro work flow describes how to view the results of Desmond simulations in Maestro describes VMD an alternate workflow available separately from the University of Illi nois that can also be used to setup simulation systems and to view trajectories and ana lyze the results of simulations provides pointers to additional documentation on Desmond Maestro system Release Notes e Note that Desmond 2 4 and higher internally utilizes a new binary input structure file These files are called Desmond Molecular System files and have the extension dms The dms file format and related information is documented in the Desmond User s Guide You do not need to consider the dms files explicitly with the sole exception of the forceconfig py setup tool described in Running Simulations from the Command Line on page 56 e You will notice that the Maestro toolbars have changed from the prior release to allow for more customization and convenience The double column main toolbar in prior releases has been split into several smaller toolbars There is anew manager toolbar that has buttons to launch toolbars including Project Edit and View Click the buttons to show or hide the toolbars You can drag toolbars to any edge of the Workspace or even place them as free standing toolbars outside the main window
117. o Fourier grids The script is called forceconfig and can be launched as follows SSCHRODINGER run FROM desmond forceconfig py lt input dms gt input dms is a binary file that is generated automatically prior to any Desmond run and is normally invisible to the user However for the purpose of using forcecon fig py one needs to generate input dms explicitly using the following command SSCHRODINGER run FROM desmond mae2dms input cms input dms where input cms can be the output structure file of System Builder or Viparr For expert users The dms file format is the native format for Desmond and the only for mat supported in the standalone Desmond source distribution If you have a dms file there is a reverse script called dms2mae that can be used the same way to convert a dms file to cms format The forceconfig script analyzes the system and outputs the recommended Desmond configuration settings The output can be copied and pasted into a custom Desmond configuration file for use with the simulation system at hand Run the script with the help option to see optional command line arguments e While a Desmond job is running all files related to the job are continuously updated in a temporary directory at job completion or if the job crashes files are copied back to the working directory D E Shaw Research 57 Desmond Tutorial 58 NOTE Running Desmond Simulations The location of this temporary directory is t
118. odify Refine Click R H A a x 20 gt 7 Ba a H bond assignment a Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image Nej e Interactive E ia Pp a gt gt 7 e c Q 0 Q 3 gt acomplia crertaions Optimizer Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color X E F X aa Minimize hydrogens of altered species Find Specified atoms v Select htrynum 868 1060 N R 0of0 X Fit Sample at pH Overy low OLow Nex Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Frag Optimize Click Analyze Network Interactive Optimizer Open panel that allows interactive manual optimization of H bond Remove waters retai interactive H bond optimine 7777 Ex Analysis mir nclude current orientations Conv PH neutral Only analyze Workspace selection Hy Analyze Network H Forced ne yee ee Use crystal symmetry Click Optimize View all species ecies total View cluster 1 30 clusters total All species The table is Optimize Degree of sampling Low High i filled with the View Pro Display result 1 cor current Lock Species State MRE protonation 64 A HOH 148 Initial states of ASP 65 A HOH 149 Initial GLU and HIS 66 A HOH 150 Initial residues as well as initial OH bond orientations 67
119. of the protein that is important System Builder Output File Format The System Builder writes the simulation system in a composite model system file with the extension cms Composite model system files are essentially multi structure Maestro files that are suitable for initiating Desmond simulations Typically the total solvated sys tem is decomposed into five separate sections in the cms file protein solute counter ions positive salt ions negative salt ions and water molecules The System Builder also writes Schr dinger OPLS AA force field parameters in the cms file You can find detailed documentation of the cms file format in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 Note that Desmond 3 0 uses a different file for mat called a dms file internally but in the Desmond Maestro environment the dms file is transparent to the user there is no need for it explicitly The dms file format is docu mented in the Desmond User s Guide Adding Custom Charges In some cases you may want to have specific charges on certain molecules in a system for example the ligand molecule You can specify custom charges in the Use custom charges section of the System Builder First you must identify the charge you want to use You can either select partial charges from a structure or you can identify the column in the Maestro input file that is storing the custom charges Second you must specify the sub
120. olecule molid molecule read molid 1 filetype mae filename struc ture cms molecule read molid filetype dtr filename trajectory dtr wait for 1 The 1 argument to molecule read indicates that a new molecule should be created for the file We specify filetype and filename to load the structure Finally we use the molid returned by the first read command as the first argument to the second read com mand so that data from the trajectory gets appended to the original structure file The waitfor 1 means to load all frames in the trajectory before returning from the call This corresponds to the Load all at once option in the File menu You can also specify a range of frames to be loaded molecule read molid dtr trajectory dtr beg 5 end 55 skip 10 waitfor 1 Assuming there were at least 55 snapshots in trajectory dtr this command would load snapshots 5 15 25 35 45 and 55 into the molecule with the given molid Getting information about snapshots Data in VMD is organized into Molecules which represent entire molecular systems as well any number of snapshots associated with those systems As molecules are loaded they are assigned an integer key called a molid Exactly one molecule at any given time is tagged as the top molecule unless you set the top molecule yourself this will always be the most recently loaded molecule Each molecule in VMD has a fixed number of atoms To each atom VMD associ
121. on object Atom selection objects are created in the VMD Python interface using the atomsel mod ule Import the atomsel type from atomsel import atomsel Create a selection corresponding to all atoms in the top molecule pointing to the current frame all atomsel Table 7 1 Summary of functions from VMD built in molecule module function result new name molid of newly created molecule listall list of available molid values numatoms m number of atoms in molecule m numframes m number of frames Snapshots in mole cule m get_top molid of top molecule 1 if none set_top m make molecule m the top molecule get_frame m get current frame of molecule m set_frame m frame set current frame for molecule m to frame get_periodic m 1 frame 1 dictionary of periodic cell data default top molecule current timestep set_periodic m 1 frame 1 set periodic cell keywords a b c alpha beta gamma get_physical_time m 1 frame 1 time value associated with timestep default top molecule current timestep read molid filetype filename load molecule files write molid filetype filename save molecule files Select just the atoms named CA i e the alpha carbons in the top molecule in the current frame ca atomsel selection name CA Select the protein atoms in frame 10 of the top molecule if the current frame changes the selection will still point
122. on page 58 30 Click Advanced Options to set parameters for the simulation Advanced options are covered in Specifying Desmond Simulation Parameters on page 51 31 Click Start The Molecular Dynamics Start dialog box appears as shown in Figure 1 17 Figure 1 17 The Molecular Dynamics Start dialog box d v Molecular dynamics Start ej x Select Append new entries to add results to the current project lt Output Incorporan Append new entries Job April 2011 32 Enter a name for the simulation job NS Select the host where the ost job should run usually localhost on a standalone workstation Click Start One job to submit for 1 simulation Name 4p ti_Des mond _md_job cpus 4 Details lt lt The system will be domain decomposed as follows xfi_jyf2_ jz Actually needs 4 CPUs simulation Stat Cancel Select Append new entries from the Incorporate option menu in the Output area to indi cate that results of the Desmond simulation should be added to the current Maestro project D E Shaw Research 17 Desmond Tutorial 33 Desmond Tutorial In this example the job will run on localhost which is typically a standalone worksta tion using 4 CPUs with a domain decomposition the number of blocks into which the simulation box will be split in the X Y and Z directions of 1x2x2 For large scale simul
123. on summary _ Properties i Job name esmond_Tutorial 0 Average Std Dev Slope ps Results of the Job progress Normal Total energy kcal mol 40236 304 6 515 0 002 analysis appear Duration ns 4 8 Potential energy kcal mol 48645 287 53 083 0 000 in this area Time ns NA Temperature K 298 691 1 092 0 000 Degrees of freedom 28540 Pressure bar 2 344 82 639 0 004 Particles 14026 Volume 3 42256 254 219 699 0 015 Atoms 14026 Target temp K 300 0 Ensemble type MTK_NPT Status None Close Help Click Browse and select the energy file desmond_job ene then click Analyze You should see similar output to that shown in Figure 6 4 The table displays useful information about simulation parameters and show the statistical properties of basic thermodynamic quanti ties based on block averaging Click Plot to display an interactive graphical representation of the data table as shown in Figure 6 5 Figure 6 5 Interactive Simulation Quality Analysis Plot Qe EEE 0 O Gia 4 022e4 1000 2000 3000 4000 5000 x 3649 19 y 126 875 You can find more details about simulation quality analysis including plotting options in the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 April 2011 D E Shaw Research 91 Desmond Tutorial Visualization and Analysis using Maestro Perfor
124. ored in columns 0 1 and 2 of the respective arrays If a frame holds no velocities then the velocities method will return None The molid argument defaults to the top molecule just like atom selections and the frame defaults to the current frame at the time the array is returned Since the arrays reference snapshot data without making a copy they must not be used after the frame to which they refer is deleted any attempt to do so will probably result in a program crash However accessing positions with vmdnumpy is far more efficient than extracting coordinates from atom selections The most efficient way to extract a subset of the coordinates corresponding to a selection is to use the atom indi ces as a Slice argument to the positions array pos vmdnumpy positions all positions in top molecule s current frame inds ca get index index of all CA atoms ca_pos pos inds M x 3 array where M len ca As summarized in Table 7 1 the periodic cell data is returned by mole cule get_periodic asa dictionary whose keys are a b c alpha beta and gamma corresponding to the lengths of the three unit cell shift vectors and the angle between b and c a and c and a and b respectively To change the unit cell by hand use molecule set_periodic with the same keyword arguments as the dictionary to change the desired attributes April 2011 D E Shaw Research 107 Desmond Tutorial 108 System Setup and Trajectory Analysis
125. panel EEL LLL gt Select Grow p Atom Residue Fragments Properties Properties 2 Define grow bond O Mutate Place Grow Pick Atoms B Select Amino acids Fragments Amino acids i from the Fragments faa ars arn ARG H ASH ASP H asn ASP cvs GLH GLU H GLN GLU option menu GLY Hie Hip His ie LeU LYN LYS H Lys mer PHE PRO SER THR TRP TyR vat Click ALA Grow Direction forward N to C i Joining Geometry trans Secondary Structure extended jei 4 Clean up the geometry by selecting Edit gt Build gt Clean Up Geometry 5 Build a solvated Desmond simulation box with the System Builder as described in step 16 on page 12 6 Open the metadynamics panel by selecting Applications gt Desmond gt Metadynamics The Metadynamics panel appears as shown in Figure 5 19 Metadynamics setup is virtually identical to molecular dynamics setup except for defining the collective variables and the height and shape of the Gaussian kernel potential April 2011 D E Shaw Research 83 Desmond Tutorial Figure 5 19 Metadynamics panel Select Load from Workspace and cli Load r Model system am Preparing Free Energy Perturbation and Metadynamics v oR Load from Workspace
126. psed Recording interval ps energy 1 2 trajectory 4 8 Ensemble class NPT v Temperature K 300 0 Pressure bar 1 01325 Surface tension bar A 4000 0 n A X Relax model system before simulation Relaxation protocol Browse Advanced Options _Start Read Wite J Reset The FEP panel is similar to the Molecular Dynamics panel and has the same functional ity but typically it is only used to write out a custom Desmond FEP configuration file If however you should load a structure into this panel the structure must have already been prepared for FEP simulations The Simulation section of the panel allows you to set a number of FEP related parame ters For details see the Desmond User s Guide and the Schr dinger Desmond User Man ual listed in Documentation Resources on page 111 Select the windows that should be included in FEP simulation NOTE FEP simulations involve many separate calculations with different values of A and it is quite possible that some of them will crash at the first try When this happens you should rerun the FEP simulation only for the failed windows The GUI lets you select the failed windows for a re run However we strongly recommend that you run all FEP jobs from their respective FEP panels such as the Ligand Functional Group Mutation by FEP panel or from the command line with input files generated by these windows Doing
127. r f Load The system contains 1945 atoms Simulation Metadynamics parameters Height 0 1 kcal mol Interval 0 09 ps Distance Angle Dihedral Pick atoms Atoml Atom2 Atom3 Atom4 Width 10 0 degrees Add Remove atom 1 Aton 2 atom 3 Atom 4 width walt 1 2 4 5 6 10 0 2 4 5 6 9 10 0 Simulation time ns total 1 2 elapsed 0 0 Recording interval ps energy 1 2 4 trajectory 4 8 Ensemble class NT v Temperature K 300 0 Pressure bar 1 01325 Surface tension bar A 4000 0 Relax model system before simulation Relaxation protocol Browse Advanced Options Desmond Developed by D E Shaw Research Start Write Reset Close Help 7 Inthe Metadynamics panel select Load from Workspace and click Load to import the solvated system from the Workspace 8 Hide the water molecules by selecting Workspace gt Display UnDisplay Atoms gt Undisplay Waters 9 Click Dihedral and Pick atoms and select the phi and psi angles in the Workspace by clicking the four consecutive backbone atoms respectively Click Add and the selected dihedrals appear in the table NOTE You can also change the height and width of the Gaussian kernel and the frequency of dropping the kernel in phase space however the default values should suffice NOTE The rest of setup is identical to running a molecular dynamics job Note however that this metadynamics
128. r Setting Up Membrane Systems Figure 2 10 Visual feedback of ion placement Click Ribbon and select Delete Ribbons from the option menu April 2011 Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help v utam E EF FUSS A RK Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tilg Aa xX AHC KS amp dT B Select Undo Redo Delete Sketcher Add Transform Adjust Create Entry Clear Save Image New Scene oe 8 G8 o aD gt Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color xv y x X X Y ind Residue number y 219 JN P 0 of 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Once you remove ee ribbons you can see the excluded region blue and the selected candidate residues red spheres Atoms 0 15797 15797 Entries 1 13 Res 1115 Chn 1 Mol 116 Chg 23 Jobs 0 0 6 15U4 A XMEAAHSKS TEECLAYFGVSETTGLTPDOVKRHLEK YGHNELPAEEGKSLWELV IEOFMDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLIL 6 ISUJ A _TANAIVGVWOERNAENAIEALKE YEPEMGKV YRADRKSVORIKARD1IVPGDIVEVAVGDKVPADIRILSIKSTTLRVDOSILTIGESVSVIKHTEPVPDP 6 ISU aa RAVNODKKNMLF SGTNIAAGKALGIVATTGVSTE IGKIRDOMAATE ODKTPLOOKLDEFGEOLSKV ISLICVAVWLINIGHFNDPVHGGSWIRGAIYYP 6 ISUJ A KIAVALAMINGLPAVITTCLALGTRRMAKKNA IVRSLPSVETLGCTSV 1CSDKTGTLTTNOMSVCKMF I IDKVDGDFCSLNEFSITGSTYAPEGEV 6 ISU4 A
129. ral Only analyze Workspace selection Find Specified atoms gt Select N Plo of 0 Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fr Analyze Network Use crystal symmetry View all species 76 species total View cluster 1 30 clusters total All species 2 Optimize Degree of sampling Low High Click the Lock option for a selection to preserve its state isplay result 1 Lock Species State 64 A HOH 148 Initial 65 A HOH 149 The workspace is focused 66 A HOH 150 m on the selection Click of inon Initial He land E to flip through s k a number of discrete a9 I A HOH 153 Orientation 23 E orientations and view ae ACHOMEISA Initialt Ee changes immediately in 71 A HOH 155 Initial om Me a the workspace 72 A HOH 156 Initial se 73 A HOH 157 Initial iv Warning BOC CCC CC C C CC CC G R G R GGG Add Orientation Sort By State A There are no problems to report Pick to locate species Atoms 3 751 1081 Entries 1 4 Res 120 Chn 1 Mol 61 Chg 6 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right Select an item in the table to focus the workspace on the selected residue For exam ple selecting item 69 in the table focuses the workspace on HOH153 as shown in Figure 1 10 Originally this water molecule is in close contact with the HE hydrogen of ARG53 By
130. ranslate right click on atom spot center right click on atom bond and hold menu System Builder saves the whole simulation system in a composite model system file with the extension cms Composite model system files are essentially multi struc ture Maestro files that are suitable for initiating Desmond simulations NOTE Maestro automatically assigns the latest OPLS AA force field parameters available in the Schr dinger Suite to the entire system If you would rather apply a Desmond provided force field such as Amber or Charmm force fields TIP5P water model etc you need to process the cms files using the external Viparr program see Generating Force Field Parameters with Viparr on page 47 Now we are ready to perform the Desmond simulation Expert users will typically want to start a simulation from the command line see Running Simulations from the Command Line on page 56 However for this tutorial we will run it from the Molecular Dynamics panel in Maestro 26 Select Applications gt Desmond gt Molecular Dynamics The Molecular Dynamics panel appears as shown in Figure 1 16 16 D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 16 The Molecular Dynamics panel Select Load from Workspace and click Load 9 Molecular dynamics o Aoa p Model system Load from Workspace v ai The system contains 14026 atoms Simulation Simulation time ns
131. red as a single trajectory file associ ated with an index file idx and the simbox dat file containing data about the simulation box Simbox information A checkpoint file that allows for the bitwise accurate restart of Desmond jobs that crashed for some rea son You can find the pertinent documentation in the Desmond User s Guide and the Schrodinger Desmond User Manual listed in Documentation Resources on page 111 Tra jectory analysis is covered in Visualization and Analysis using Maestro on page 87 and System Setup and Trajectory Analysis Using VMD on page 95 D E Shaw Research April 2011 2 Preparing a Desmond simulation with the System Builder Overview The System Builder is a graphical tool in Maestro that lets you generate a solvated system for Desmond simulations You can launch the System Builder by selecting Applications gt Desmond gt System Builder as shown in Figure 2 1 Figure 2 1 Launching Desmond System Builder Select Applications gt Desmond gt System Builder April 2011 Maestro Project Edit View Workspace Tools emt 2 A Open Save As Import Export Table 2D Viewer Lig M X K HG eain tindalDeda Nalsta Cketrhar_AddH Tranefar s6 G 00 Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Y Yv X v Y Y x Select Find Specified atoms En Pe ae Perea Task View CombiGlide gt ConfGen Core Hopping gt
132. ree Energy Perturbation and Metadynamics Creating a Custom Fragment Group NOTE April 2011 For details see the Desmond User s Guide and the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 There is a Python script available which can be used directly to compute the free energy difference associated with a FEP job the script is run by default as part of an MultiSim workflow The following script will process the energy file output of the different A runs and compute the free energy SSCHRODINGER run FROM desmond bennett py Use the help option to learn about the use of this script and consult the Desmond User s Manual listed in Documentation Resources on page 111 for more details Creating a Custom Fragment Group If the Fragment Library does not have the mutant structure you want to use you can edit any pre defined substitution group manually using the general Build Edit tools in Maestro The only caveat is that the customized substitution group will retain the name of the frag ment that you modified However the FEP simulation will use the modified fragment Use caution with custom fragments Any mutation that involves more than a few atoms is likely subject to very large uncertainties in the free energy differences computed between different lambda windows Try decomposing a large mutation into several small muta tions and run multiple MultiSim FEP simulations It will take long
133. ries 2 0 ee en 96 Loading Files from the Command Line 0 0 96 Loading Files from the GUI 2 0 ee ee 97 Loading files from the scripting interface 0040 104 Getting information about snapshots 2 6 ee 104 Atom selections ooa a 105 SMAPSHOtS g pe aE KA E E teal E E A E RE ETA E a ea 107 Centering trajectories oaoa eee 108 Writing structures and trajectories o oo ee 108 Analyzing whole trajectories 2 a 108 8 Documentation R SOUICES 00 cc ee 111 vi D E Shaw Research April 2011 List of Figures April 2011 Figure 1 1 Simulation Process cccccseccceseseescscseseseecsesesesescecessssnecssecssensnesesesessneneeesenes 3 Figure 1 2 Maestro main environment cccccceeseesesesescssesesceesesenssseecseeeesecsesesssesseseeeeeees 4 Figure 1 3 Import dialog Dox vicississesscsesosessacnanssoscsstennsesonssonaa stusveotas onstseobodstenseesigonstsnonoesests 4 Figure 1 4 Get PDB File dialog DOX ccc ce cence cecesesseseesecsssnsnesesssessneseseeseeees 5 Figure 1 5 Imported protein structure file occ sec cesses ceeeeseseecscseseseececsessenseeeeees 6 Figure 1 6 Changing from ribbon to ball and stick view sssssessessessessessisssesesresieseesee 7 Figure 1 7 Protein Preparation Wizard panel ccccc cesses es eesseseeeecsseeeseeeteteeeeeeees 8 Figure 1 8 Protein Preparation Wizard Preprocessing stage 0 0 eee eseeeeees 9 Figure 1 9 Prot
134. rstertestesse tes 27 Figure 2 6 The 1su4 structure in standard orientation s sessssessssesrtsessssstssrtestessseestess 28 Figure 2 7 The Ions tab in the System Builder panel ssssssssssssssessssssssisessessessiesresressesens 29 Figure 2 8 Selecting the excluded region se sssssssssssissesssssisreesesstssiesresissesntestestesressenees 29 Figure 2 9 Placement of the counterions sssssssssesiesessessessierissesstssiesiesiesensrestestesressenees 30 Figure 2 10 Visual feedback of ion placement sssssssssrsssssssstsssserttssserstesssesresnteeseesneees 31 Figure 2 11 Set Up Membrane dialog bOX s ss ssssssssssssssissessessiesieseesenssesinseesensensnenrenressesses 32 Figure 2 12 Selecting transmembrane residues se sssssssssssesseesesssestesteserssestestesressestes 33 Figure 2 13 Importing the selection into the Atom Selection dialog box s 12512 34 Figure 2 14 Initial automatic membrane placement for 18U4 s sssssssssssissssssesiesrerressesses 35 Figure 2 15 Adjusted position of the membrane for 1SU4 sssssssssesissessessssiestersessesses 36 Figure 2 16 Final simulation system for 1SU4 wo cece cc eeeeeececseseseeeecsssneseseneees 37 Figure 2 17 Transmembrane hole in the POPC bilayer for 18u4 oo eee 38 Figure 2 18 The OPM Home page cccccccseceeeeescscseeeseecscesessssescecssessnesesessssssneseseanes 39 Figure 2 19 Downloading the OPM pre aligned coordinates 00 ccc eee 40 F
135. s NPT or NVT are run with reasonable default settings but user defined workflows can also be imported This option is the least flexible but most convenient solution Figure 5 6 FEP workflow control Iw Ligand Functional Group Mutation by FEP G G ao X Define Perturbation Plan Calculation r In complex Select Use lambda P e hopping to enhance the relative binding free energies sampling to improve FEP protocol Desmond NPT 7 ae convergence See the Buffer size A 5 0 Production simulation time ns 0 6 Schr dinger Desmond Use lambda hopping to enhance sampling User Manual for y In pure solvent information This calculates the relative free energy for each ligand mutant in the pure solvent environment The results are needed to derive the relative binding free eneraies and the relative solvation free enerales Select the FEP protocol FP protocol Desmond NPT that will be used during simulation Buffer size A 10 0 Production simulation time ns 0 6 r C In vacuum This calculates the relative free energy for each ligand mutant in vacuum The results are needed to derive the relative solvation free eneraies ee ction simulation time ns 2 0 Desmond Developed by D E Shaw Research Start _ _ Write Reset Close Help NOTE Lambda hopping is a form of replica exchange in which coordinate exchanges o
136. s achieved by periodically drop ping repulsive kernels of Gaussian shape at the current location of the simulation in the phase space of the collective variables This history dependent potential encourages the system to explore new values of the collective variables and the accumulation of poten tial allows the system to cross potential barriers much more quickly than would occur in standard dynamics Metadynamics is fully documented in the Desmond User s Guide listed in Documentation Resources on page 111 In this Tutorial we present a simple working example to get familiarized with metady namics The example involves generating the well known 2 dimensional free energy surface of alanine dipeptide with respect to its phi and psi dihedral angles Follow these steps to generate and plot the free energy surface 1 Build alanine dipeptide in Maestro a Open the fragment library panel by selecting Edit gt Build gt Fragments On the Fragments tab of the Build panel select Grow select Amino acids from the Fragments option menu and click ALA in the table as shown in Figure 5 18 c Close the Build panel The alanine dipeptide molecule appears in the Maestro Workspace Alanine dipeptide is in fact a single alanine molecule with capping groups ACE on the N terminus and NMA on the C terminus D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Aside Metadynamics Figure 5 18 Fragment library Build
137. s py help will list more options Importing a Simulation System from the Amber Molecular Dynamics Package If you have developed simulation systems using Amber Molecular Dynamics package http ambermd org you can import these systems into the Desmond environment Des mond includes a command line script for converting an Amber prmtop file and associ ated crd file into a Desmond cms file The script is called amber_prm2cms and can be launched from the command line as follows S SCHRODINGER run FROM mmshare amber_prm2cms py p my_amber_system prm c my_amber_system crd o output cms The two input files should be standard Amber prmtop and crd files respectively and the output file is the Desmond cms file Since Desmond reads the force field parameters directly from the cms file it is guaranteed that Desmond will apply the exact same force field in one to one agreement with the Amber prmtop file Specifying Desmond Simulation Parameters Before it can perform simulations Desmond needs certain simulation parameters to be set These parameters can be set in two ways e Using one of the Desmond applications in Maestro e Editing the Desmond conguration file directly The following sections provide more details on each option Using Desmond applications in Maestro There are several Desmond applications available in Maestro from the Applications gt Desmond menu The applications include minimization molecular dynamics sim
138. salt ions will be randomly distributed in the entire solvent volume of the simulation box excluding of course the volume occu pied by the solute and if present the lipid bilayer e The type of positive or negative ions to use can be specified in the lons tab Figure 2 3 lons tab in Desmond System Builderpanel 24 v Bonu eee 8 x Solvation tons Excluded region Exclude ion and salt placement within A of Select Clear lon placement You can choose to neutralize add Oe i l a specific number of counterions Neutralize by adding 6 cl lv ions Recalculate F Add Na ions or not add any counterions e Advanced ion placement You can set the concentration of SE Add salt salt to add and choose the type of ae e LE positive or negative ions Salt positive fon Uva Salt negative ion Cl v Force field OPLS2005 ibd Start Write Reset Close Help D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Generating the Solvated System Generating the Solvated System NOTE NOTE At this point you can generate the solvated system by clicking Start in the System Builder panel After this task has completed the solvated system will appear in the workspace see Figure 1 15 on page 16 and the resulting system which is ready for Desmond simu lation will be written to a cms file see System Builder Output File Format on page 23
139. set of atoms D E Shaw Research 23 Desmond Tutorial Preparing a Desmond simulation with the System Builder for which the custom charges will be applied using the Select panel The rest of the atoms will be assigned standard OPLS AA charges Adding lons Click the lons tab in the System Builder panel as shown in Figure 2 3 to add ions to your system By default the System Builder automatically neutralizes the solute For example if the solute has a net charge of N System Builder will randomly select N residues on the surface of the protein with a positive formal charge and respectively place a nega tive counterion in the vicinity of the selected residue For negatively charged solutes positive counterions will be similarly positioned Click Advanced ion placement to place counterions in a more sophisticated manner this procedure is illustrated in Setting Up Membrane Systems on page 25 where membrane setup is discussed using a concrete example You can also define an excluded region in the Select panel where neither coun ter ions nor salt ions are allowed e An arbitrary number of counterions can be added for example if there is a reason not to neutralize the system refer to the special note in Setting Up Membrane Sys tems on page 25 Conversely you may choose not to place any counterions e Background salt can be added to the system by specifying the salt concentration in the Add salt section in the lons tab The
140. simulation box appears in the workspace as shown in Figure 1 15 For better clarity the 4pti structure is shown as a CPK model The solvated simulation box will appear off centered with respect to the red boundary box This is because the System Builder re centers the system To produce the view in Figure 1 15 turn off the Show boundary box option in the System Builder panel Figure 1 12 and click the Fit to Workspace icon circled in Figure 1 15 D E Shaw Research 15 Desmond Tutorial Desmond Tutorial Figure 1 15 Solvated protein structure in the workspace 7 Maestro 4pti prj Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help oe amp g H PDB 5 38 e uram Bmx TF SS A S amp Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz if Fog Enhance Rotate X Rotate Y Tile La r n mw oy X HK HPA ee a b Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene c tel s 5 0 2 8 2 gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color Y voy X X x Y Find Residue number y 219 N P Oof 0 Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments For clarity the protein structure is shown as a CPK model Atoms 0 13696 14026 Entries 1 5 Res 4425 Chn 2 Mol 4396 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy t
141. simulation should run for 1 2 ns to achieve convergence NOTE Metadynamics is also supported via MultiSim More complicated collective variables via generic ASL expressions can be set using MultiSim and command line execution 10 When the job finishes select Applications gt Desmond gt Metadynamics Analysis The Metadynamics Analysis panel opens Click Browse and open the desmond_metadynamics_job out cfg file or the corresponding out cfg file if you 84 D E Shaw Research April 2011 Preparing Free Energy Perturbation and Metadynamics Aside Metadynamics provided a custom name for the job Reading the data will take a few minutes Then the free energy contour plot appears as shown in Figure 5 20 Figure 5 20 Metadynamics Analysis panel T Analysts O Input file fground build16 Desmond_Tutorial 0 6 desmond_metadynamics_job out cfg A A rat lt B x 80 2278 y 139 045 120 10 5 N 9 0 G 60 75 amp g D o 60 5 s amp 2 2 T 45 5 v 60 3 0 a L5 120 0 0 180 J 180 120 60 0 60 120 180 Dihedral degrees CV1 Plot Options C Show Grid 2 Offset to zero Angle units degrees v Read Plot Data Write Plot Data Close Help Consult the Schr dinger Desmond User Manual listed in Documentation Resources on page 111 for details on manipulating the plot and exporting the free energy data April 2011 D E Shaw Research 85 Desmond Tutori
142. skip 10 waitfor 1 This command would write every 10th frame starting from frame 100 Coordinates can also be written using an atom selection sel atomsel name CA sel frame 45 sel write mae ca45 mae This command would create write a Maestro file containing just the CA atoms whose coordinates were taken from frame 45 Analyzing whole trajectories We can now give a nontrivial trajectory analysis example that illustrates the use of atomsel vmdnumpy and molecule The script shown in Figure 7 12 runs through all the frames in a molecule aligns each frame to the first frame and computes the aligned RMSD for each frame and the averaged position of the alpha carbons To use this script it s necessary to load the reference structure and any trajectories to be processed into VMD using any of the methods outlined in Loading and Viewing Trajectories on page 96 D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Analyzing whole trajectories Once that s done you can launch the script as described in The VMD Python Interface on page 95 Figure 7 12 Analysis script example April 2011 from atomsel import atomsel import molecule vmdnumpy import numpy avg None will hold averaged coordinates all atomsel all atoms in current frame ref atomsel name CA frame 0 reference frame is frame 0 sel atomsel name CA alpha carbons in current frame inds sel ge
143. so allows the FEP simulation to run via the MultiSim system which has a built in automatic recovery mechanism with this recovery mechanism you can restart a failed job from the MultiSim checkpoint file 3 Write out the Desmond conguration file by clicking Write April 2011 D E Shaw Research 69 Desmond Tutorial 70 NOTE Preparing Free Energy Perturbation and Metadynamics Running FEP Simulations from the Command Line FEP simulations can be run from the command line using a msj command script file in exactly the same way as described in Running MultiSim jobs from the Command Line on page 58 SSCHRODINGER utilities multisim JOBNAME lt jobname gt maxjob lt maxjob gt cpu lt cpu gt HOST localhost SUBHOST lt hostname gt i lt jobname gt mae m lt jobname gt msj o lt jobname gt out mae where e lt jobname gt is the name of the job e lt maxjob gt is the maximum number of subjobs that can be submitted to a host or a queue simultaneously A value of zero means that there is no limit e lt cpu gt is the number of CPUs per subjob which can also be specified as e g 2 2 2 note the quotes indicating 8 CPUs with a spatial decomposition of 2x2x2 e HOST localhost means that the master job runs on your local workstation whereas e lt hostname gt given with the SUBHOST option is the name of the host or queue where the simulation jobs will be running When MultiSim is used for
144. structure Set Atom number Atom number Add Subtract Intersect Update Markers Atom type MacroModel Atoms matching Hydrogens fo Ey PDB B temperature factor Examples Formal charge lt 12 or 3 5 20 34 Partial charge R rk 7 Number of attachments ange A WOnSpace Display state 1 15797 Backbone side chain PDB serial seqres index ASL X Show markers atom num 312 313 314 315 316 317 318 319 320 321 322 323 a 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 z Proximity 366 367 368 369 370 371 372 373 374 375 376 377 378 379 ma H H a 320 321 382 323 324 385 326 387 388 389 309 391 397 393 7 Create Click Selection All Undo Redo Clear Invert Previous Selection lt arom Num Res Num Matching 6182 atoms ok Cancel Help When the ASL area is filled click OK At this point the ASL area will be filled with the selection in the Set Up Membrane dialog box Click Place Automatically as shown in Figure 2 11 on page 32 and the resulting membrane placement will appear in the workspace as shown in Figure 2 14 As you can see the membrane positioning needs minor adjustment NOTE Switch back to ribbo
145. t 7 fluoro c Reset 8 chloro Reset 9 hydro Reset Desmond Developed by D E Shaw Research l Start Write Reset Close Help J D E Shaw Research Creating a Custom Fragment Group 73 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics Figure 5 10 The intermediate methyl substitution group shown in the workspace The methyl substitution group is shown in the workspace 74 r v Maestro Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help U oaam E PF FoG A S F Open Save As Import Export Table 2D Viewer Lig Int GetPDB Prep Wiz Fit Fog Enhance Rotate X Rotate Y Tile min X KH SF MS amp FH amp Select Undo Redo Delete Sketcher Add H Transform Adjust Create Entry Clear Save Image New Scene X c9 2 8 Q D gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color voy x v X X X R P A gt Li Ce W BE A e A o gt Ns lt D gt Draw SetElement Bond Order Bond Order Formal Chg FormalChg Move R S Cleanup Sculpt Find Atom number X NPO of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 j middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu Open the fragment
146. t SUBHOST lt hostname gt i lt jobname gt cms m lt jobname gt msj o lt jobname gt out cms where e lt jobname gt is the name of the job e lt maxjob gt is the maximum number of subjobs Desmond simulation jobs of any kind that can be submitted to a host or a queue simultaneously A value of zero means that there is no limit e lt cpu gt is the number of CPUs per subjob which can also be specified as e g 2 2 2 note the quotes indicating 8 CPUs with a spatial decomposition of 2x2x2 e HOST localhost means that the master job runs on your local workstation e lt hostname gt given with the SUBHOST option is the name of the host or queue where the simulation jobs will be running e c lt config_file gt is an optional argument used to set non default Desmond configuration parameters e mode umbrella is the default option when a MultiSim job is run on a cluster MultiSim jobs include a cascade of consecutive subjobs each of which requires a new CPU allocation depending on the availability of cluster resources this can D E Shaw Research April 2011 Running Desmond Simulations Running MultiSim jobs from the Command Line April 2011 NOTE NOTE involve a significant time lag The mode umbrella option instructs the cluster job submission system to recycle allocated CPUs thus providing better job turnaround time The input files include a cms file which is the output file of the System Bui
147. t index indexes of alpha carbons don t change mass sel get mass masses don t change either rms 0 will hold RMSD to reference frame 4 4 4 4 def processFrame global avg all move sel fit ref mass Align current frame w ref frame rms append sel rmsd ref mass Append new RMSD value Get positions of CA atoms pos vmdnumpy positions ca_pos pos inds Accumulate positions into average if avg is None avg ca_pos make a copy of ca_pos else avg ca_pos add this frame s contribution Loop over frames n molecule numframes molecule get_top for i in range 1 n molecule set_frame molecule get_top i processFrame Scale the average avg n D E Shaw Research 109 Desmond Tutorial System Setup and Trajectory Analysis Using VMD This page left intentionally blank 110 D E Shaw Research April 2011 April 2011 Documentation Resources Detailed Desmond documentation can be found in the D E Shaw Research Desmond User s Guide The Desmond user community website provides an interactive user forum for exchanging Desmond related information http groups google com group desmond md users You must register with the group but this is done by simply applying for group member ship on the site Once you are a member you can search the forum and post comments as well as browse the Desmond MD Users site which provides additional Desmond resources such as FAQs
148. t Table 2D Viewer Lig int GetPDB PrepWiz Ft Fog Enhance RotateX RotateY Tilg fa e r t al HY X KH OF KM w s a Select Undo Redo Delete Sketcher AddH Transform Adjust Create Entry Clear Save Image New Scene ak 2 X X X A 5 766 6 O O gt Ribbon Wire CPK Ball amp Stick Tube Thin Tube Color Scheme Color z y F zo r Dd Y E t Gi Gi a mM NEMA Draw SetElement Bond Order Bond Order FormalChg FormalChg Move R S Cleanup Sculpt Find Atom number X uiP O of Fit Project Edit View Workspace Style Saved Views Display Atoms Representation Labels Build Fragments Unfavorable contacts AL are shown in red are shown in orange Atoms 0 0 67 Entries 1 9 Res 1 Chn 1 Mol 6 Chg 0 Jobs 0 0 middle xy rotate ctrl middle z rotate right xy translate right click on atom spot center right click on atom bond and hold menu 3 To arrive at a suitable conformation of the substitution group you must adjust the tor sion angle and often multiple angles You can alter the torsion angle manually by holding down the left mouse button and moving the mouse horizontally or by rotat ing the mouse wheel Try relaxing the unfavorable contacts with rotations about dif ferent bonds in the buty1 side chain You should arrive to a conformation similar to that shown in Figure 5 16 As you can see in Figure 5 17 the altered buty1 conforma tion is now fairly close to that of the original NH CH C
149. t selections Step 3 Segments Identified Name Length Index Range Nter Cter Type Add a new chain Edit chain Delete chain Create chains Step 4 Patches Patch Segid Resid Segid Resid DISU P1 5 P1355 x Add patch DISU P1314 P1338 DISU P1 30 P1 51 Delete patch Apply patches and finish PSF PDB Reset Autopsf I m feeling lucky 3 Click I m feeling lucky at the lower right corner of the AutoPSF window to complete the automatic setup Default settings in Step 1 through Step 4 should work if you want to change any parameter please consult the VMD documentation The solvated pro tein should appear in the VMD Display as shown in Figure 7 10 102 D E Shaw Research April 2011 System Setup and Trajectory Analysis Using VMD Loading and Viewing Trajectories Figure 7 10 The solvated 4pti structure in VMD Figure 7 11 April 2011 AJ Vii 1 8 7a58 OpenGL Display Make sure that the last molecule in the VMD Main window is selected and select File gt Save Coordinates as shown in Figure 7 11 Set the file type to mae and click Save Give a name to the Maestro output file in the file browser and click OK You can also write out the Maestro file by issuing the following command from the VMD text window vmd gt animate write mae my_output_file mae Saving the 4pti system in Maestro format PSU pets Atoms Frames Vol Load Data Into Molecule Sel
150. teins in OPM 1023 entries 1su4 Calcium ATPase E1 2Ca state Hydrophobic Thickness 29 5 2 2 Protein Links Tilt Angle 26 0 PDB Sum PDB OCA MPKS PDBTM MPDB AGtransfer 66 4 kcal mol 3D view in Chime Jmol P or Webmol SBCB Links to 1su4 PDB Sum amp SCOP MSD P OCA MMDB amp Dali P Click Download j Coordinates Topology subunit A N terminus cytoplasmic Tanalaa in Fadanlacmir reticulum In Maestro click Broom in the Workspace toolbar to clear the workspace 4 Import the 1su4_opm pdb file by selecting Project gt Import Structures Maestro will issue a warning but ignore it As you can see on Figure 2 20 the reason for the warning message is the presence of two sets of dummy atoms in the PDB structure shown as layers of colored disks in the workspace These dummy atoms designate the positions of the lipid head groups in the OPM database Note that the system is shown in a similar orientation that we used in the previous exercise for better comparison not the official OPM orientation shown in Figure 2 19 40 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Importing Membrane Placement from the OPM Database Figure 2 20 Importing the OPM PDB file in the workspace bg Maestro Maestro Project Edit View Workspace Tools Applications Workflows Scripts Window Help v uram Ee F SSeS A port Table 2D Viewer Lig Int G
151. th previously specified force field several can be listed each preceded by its own m nFFIO_NAME force field name to put into output file pPLUGINDIR override for plugins directory advanced usage xX do not print header info for testing purposes V verbose output The built in force fields include the latest versions of Amber CHARMM and OPLS AA families of fixed charge force fields Viparr also provides the parameters for all SPC and TIP families of water models A simulation system or chemical system is described using a number of structures called connection tables that reside in CT blocks in the cms file These CT blocks are designated by the _m_ct structure and are composed of a number of chains which in turn are composed of a number of residues for our purposes residues may be something other than amino acids for example water molecules or ions Viparr matches residues in the chemical system to templates in the force fields Viparr uses atomic numbers and bond structure to match residues to templates Thus if there are non standard atom or residue PDB names in the cms file there is no need to modify them to match the names used in the force field You can freely modify atom and residue names for historic idiosyncratic or any other purposes In particular Viparr will identify the N and C terminal versions of the residues correctly as well as protonated deprotonated versions of a residue even if the
152. the current contents of the workspace to constitute the sol ute Note that some parts of the structure in the workspace may not be displayed but are still included in the solute Supported solvent models in the GUI include SPC TIP3P TIP4P and TIP4PEW water additionally Viparr allows TIP5P see Generating Force Field Parameters with Viparr on page 47 Organic solvent boxes for DMSO methanol and octanol are also available through the System Builder Furthermore custom models are also allowed if you can provide the location of a pre equilibrated box of a different solvent molecule Defining the Simulation Box When defining the simulation box the goal is to reduce the volume of solvent while ensuring that enough solvent surrounds the solute so that the protein does not see a periodic image of itself during simulation Too much solvent will unduly lengthen the computation One way to minimize solvent volume is to select a shape for the simulation box that is similar to the protein structure The System Builder shown on Figure 2 2 supports all D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder System Builder Output File Format April 2011 NOTE standard box shapes cubic orthorhombic triclinic truncated octahedron and so on Select the most appropriate shape from the Box shape option menu in the Boundary condi tions section of the Solvation tab and click Calculate if you want to comput
153. ther Load from the Workspace or Import from file and select a cms file and then click Load The import process may take a few seconds for large systems The basic settings shown in Figure 3 1 include Simulation options Include simulation time simulation intervals time intervals by which different energy terms are recorded and trajectory snapshots are saved and ensemble class NVE NVT NPT NPAT and NP YT Model relaxation Select Relax the model system before simulation You can either use a default protocol which includes a series of pre defined minimizations and molecu lar dynamics executions to relax the system before the production simulation starts or you can import your own relaxation protocol The stage wise relaxation equili bration tasks can be defined in a so called multisim script file which allows for run ning multiple simulations The syntax of multisim msj file is documented in the Schrodinger Desmond User Manual Relaxation and equilibration of membrane systems requires extra care to prevent water molecules from diffusing into initial voids between the membrane protein and the lipid bilayer as shown in Figure 2 17 on page 38 and Figure 2 25 on page 45 The Desmond Maestro distribution includes a special script that can be used to generate a custom relaxation protocol that you can then import to the Molecular Dynamics panel Run the following command from the command line to generate a suitable relaxation protocol
154. this stage is skipped The File tab at the bottom of Figure 1 18 shows the log file of the master multisim job It shows the actual command that is executed and details of the run The job summary is shown in the Details tab of the Job Monitor panel shown in Figure 1 19 The most useful information is the list of job IDs required in case a failed job has to be debugged The results of the simulation are saved in multiple files also listed in the Details tab D E Shaw Research April 2011 Desmond Tutorial Tutorial Steps Figure 1 19 List of files in the Monitor panel E ON drdws0086 0 4d7a4b03 4pti_desmond_setup incorporated finished 0 2011 03 11 11 17 07 d drdws0086 0 4d7bc9a5 4pti_Desmond_md_job incorporated finished 0 2011 03 12 14 29 41 d 0 4d 4pti_Desmond _job_2 completed 0 12 d drdws0086 0 ad7bca6e 4pti_Desmond md_job_3 completed finished 0 12 d drdws0086 0 4d7bcacb 4pti_Desmond_md_job_4 completed finished 12 12 d drdws0086 0 4d7bcbc9 4pti_Desmond_md_job_5 completed finished 0 12 d drdws0086 0 4d7bcc92 4pti_Desmond_md_job_7 completed finished 0 12 d drdws0086 0 4d7bcd57 4pti_Desmond_md_j completed finished C 12 d drdws0086 0 4d7bce74 4pti_Desmond_md_job completed finished 0 2011 03 12 14 50 12 d J J nma Show Jobs from this project only r Monitor frequency fi i z sec Monitor Pause Resume stop
155. to run Desmond simulations see Specifying Desmond Simulation Parameters on page 51 This simple example already shows a very useful feature of Viparr it can be used to spec ify multiple force fields In this case each residue in the chemical system matches a tem D E Shaw Research 49 Desmond Tutorial 50 Finishing Preparations for Desmond Simulation plate in exactly one of the specified force fields This means that the protein residues and the two calcium atoms will be assigned CHARMM 27 parameters whereas the water molecules get SPC parameters The command line invocation for assigning the same protein parameters but a different water model of TIP4P appears similar to this viparr py f charmm27 f tip4p 1su4_desmond cms 1su4_desmond_out cms You can also use multiple force fields to combine components of two or more force fields In this case residues in the chemical system match templates in more than one of the specified force fields In this operation mode all matching force fields are applied For example one force field provides the angle parameters for a set of residues while another force field provides the dihedral parameters for the same residues The force field components should be disjoint so there is no conflict with the parameters that are assigned to each component You may also use multiple force fields when parameters assigned to a particular residue by one force field override parameters assigned b
156. to run on your host queue at the same time You can control this parameter in the Start dialog box by setting the maximum number of subjobs as shown in Figure 5 5 The value zero means no limit In this example the master multi sim job will run on localhost local workstation whereas the subjobs the individual Desmond FEP simulations will run on a cluster via a submission queue called swdev which provides a total of 112 CPU cores Out of the 112 only 32 cores will be used simul taneously 4 FEP simulations running at the same time each utilizing 8 cores Note that the total number of FEP simulations is 24 by default 12 lambda windows for both mutating the ligand in the enzime ligand complex and mutating it in pure solvent respectively moreover each FEP simulation involves an independent relaxation proto col FEP simulations are computationally very expensive Figure 5 5 Ligand Functional Group Mutation by FEP Start dialog box 66 NOTE NOTE NOTE AY Ligand Functional Group Mutation by FEP Start Y S Output Incorporate Append new entries v Master job 2 master jobs to submit for In complex and In pure solvent calculations Name Ligand_fep_job Host localhost 4 bd Use the subjob host Subjob Host swdev 112 v CPUs subjob 8 The system will be domain decomposed as follows x 2 y 2 z 2 Actually needs 8 CPUs subjob Control how many simultaneous i simul
157. tory Player file The mdsim trajectory center option is performed at run time resulting in a centered trajectory file Refer to the Desmond User s Guide for information Additional trajectory manipulation options are available from the command line as shown next The first The first utility can be used to concatenate multiple trajectories and the second utility to extract selected frames of trajectory into a series of output structure files Use the help o SCHRODINGER run FROM desmond manipulate_trj py ption for more details SSCHRODINGER run FROM desmond trajectory_extract_frame py Figure 6 2 The Trajectory Player April 2011 v bees lll VOT Play eodocoos Control the frame for the Frame control Trajectory Player with these Pi Blt options Frame 0 of 1000 Step 10 Time 0 000 of 4 800 dns Control the display of the E bos Trajectory Player with these Speed g options Click Update secondary _____ structure to display correct ribbon rendering throughout the trajectory movie Display Cluse lower quality drawing to speed up play Update secondary structure X Show simulation box 8 Show axes Replicate system a fz b Trajectory smoothing Positioning ODo not adjust 7 a Select Center molecules to peers nites e center in the simulation box the part of the molecular system defined in the
158. type Molecule list Wwater 117 Update Markers Atoms matching 1778 ASL X Show markers res pt DUM Proximity Create Set __all__ __ Undo _ __ Redo Clear Invert Previous Selection Atom Num Res Num Matching 1778 atoms OK Cancel Help 8 Click Add and then OK and both disks will disappear from the workspace These atoms are not necessary for building the membrane The protein in 1su4_opm pdb is placed in a coordinate system such that the membrane should be aligned at d 2 along the Z axis where d is the distance between the two sets of head groups in the bilayer For 1su4 the value of d is 29 6 Angstrom 9 Preprocess the remaining system with the Protein Preparation Wizard exactly as was done in the previous exercise shown in Figure 2 5 on page 27 Do not forget to delete the sodium ion and ignore or cancel any warning messages The total charge of the system is 27 as opposed to 23 because the OPM database has a few residues in a different protonation state than the original 1su4 entry in the PDB database 10 Launch the System Builder by selecting Applications gt Desmond gt System Builder and set the solvation and ion placement options 11 Open the Set Up Membrane dialog box Click Place on Prealigned Structure as shown in Figure 2 22 D E Shaw Research April 2011 Preparing a Desmond simulation with the System Builder Importing Membrane Placem
159. ulated annealing free energy perturbation FEP replica exchange and metadynamics In this tutorial we will focus on molecular dynamics and FEP and give a simple example of metadynamics Minimization is typically used in system relaxation which will be covered Simulated annealing and replica exchange require very similar D E Shaw Research 51 Desmond Tutorial Finishing Preparations for Desmond Simulation setup to molecular dynamics and are both documented in the Desmond User s Guide and in the Schr dinger Desmond User Manual The Molecular Dynamics panel appears as shown in Figure 3 1 Figure 3 1 Setting up a Desmond simulation 52 Choose either Load from t ad from workspace f Workspace or Load from file The system cortz Click Load Set simulation options Hi X Relax model system before simulation Relaxati tocol Browse Select Relax model system ee 1 i before simulation Advanced Options Desmond 7 Molecular dynamics Model system u26 atoms ulation Simulation time ns total 1 2 elapsed 0 0 tf Recording interval ps energy 1 2 trajectory 4 8 Ensemble class NPT iz Temperature K 300 0 __ Surface tension bar A 4000 _ Pressure bar 1 01325 Developed by D E Shaw Research __ Start Read Write Reset Close Help Import the model system into the Molecular Dynamics panel by clicking Load select ei
160. ule structures always stay together for visualization purposes even if their primary images separate due to the periodic bound ary conditions In earlier versions of Desmond this separation which of course does not affect the simulation itself caused unsatisfactory visual artifacts in trajectory view ing e Misc Provides control over miscellaneous parameters including the definition of atom groups Atom group definitions are documented in the Desmond User s Guide listed in Documentation Resources on page 111 Atom groups include thermostat groups energy groups associated with Desmond s vrun application frozen atoms etc Note that atom groups are assigned in the cms structure file A frozen atom group means a set of atoms that move together during the entire MD simulation as a rigid body In Desmond unfrozen atoms cannot be connected to frozen atoms For example an entire molecule can be frozen during equilibration but one cannot freeze only the heavy atoms or just certain residues In that case restraints should be used Also note that frozen atoms cannot be used with NPT simulations because the Virial will be incorrect The other atom group termed energy is used to define parts of the system whose interaction energies can be monitored during a simulation by application of the energy groups plugin which is documented in the Desmond User s Guide Atom groups can be selected the same way as restraint groups using
161. v minimizina its transfer enerav from water to the 2 Click Download Coordinates on the search result page as shown in Figure 2 19 In the file browser give the name 1su4_opm pdb and save the file in your directory D E Shaw Research 39 Desmond Tutorial Preparing a Desmond simulation with the System Builder Figure 2 19 Downloading the OPM pre aligned coordinates Iv 1su4 Calcium ATPase E1 2Ca state Orientations of Proteins in Membranes OPM database Mozilla Firefox File Edit View History Bookmarks Tools Help gt htp opm phar umich edu protein php search 1su4 Gy fi Most Visitedy 6 CentOS Supporty UNIVERSITY OF MICHIGAN COLLEGE OF PHARMACY MOSBERG LAB ientati OPM _ o Ka in membranes a bas name samom HOME ABOUT OPM DOWNLOAD OPM FILES CONTACT US LIPID COMPOSITION ATLAS Protein Classification 2LSU4 Calcium ATPase E1 2Ca state Types 4 types Type 1 Transmembrane 2 classes Classes 11 classes Class 1 1 Alpha helical transmembrane 59 superfamilies Superfamilies 226 a Superfamily 1 1 08 P type ATPase P ATPase 1 family superfamilies 3 A 3 TCDB Families 330 families Family 1 1 08 01 P ATPase 10 proteins 3 4 3 TCDB Species 319 species a Species Oryctolagus cuniculus 14 proteins fi ion ticull i Localization 22 types a Localization Endoplasmic reticulum membrane 52 proteins All pro
162. y Player c cssicvscctssiveverovsesnsvsne eeina a E E 89 Figure 6 3 Workspace view for trajectory visualization 0 ccccceeeeeteteteseeteteseseeeenes 90 Figure 6 4 Simulation Quality Analysis panel cccccccsseseccssesesescscseeseecscsnsnseeeeees 91 Figure 6 5 Interactive Simulation Quality Analysis Plot ccc eect eeeeeeees 91 Figure 6 6 Simulation Event Analyis panel cece cece cesseseeeecessseeeeetetesseeeees 92 Figure 7 1 Loading files from the GUI oo ccccesesescceseseecscseseseseecscseseseececsssnenseessees 97 Figure 7 2 Loading the Maestro file ccccccccccsesesescscscseseseecscsesnseseecscssseseesesessneseseseses 98 Figure 7 3 Loading trajectory data cssscccssnssesesessnstoveressnvsvvensnonvavtocesonveanshogosveutetegsevocests 98 Figure 7 4 VMD Trajectory Player ccccccsesecccseeescscscseseseecsssesnecscecesessnesesesensneseseeeses 98 Figure 7 5 VMD OpenGL Display sssicc sectesisscserseelsseneds rse ese it nre ike Saris anera 99 Figure 7 6 VMD Analysis tools ses ssssssssessessesssssessessesssssensinseesesssnniesiesensnnntentesesseeneeneesee 99 Figure 7 7 VMD Modeling tools ccccccccceeeeseeceeseseececseesessnececssessnesesesesaneneseseenes 100 Figure 7 8 Loading 4pti pdb into VMD ss ss ssesssssssssssesseesessiesissresensseninseesensnnsnenrensesresses 101 Figure 7 9 VMD AutoPSF Window occ iaer ura Ri ar 102 Figure 7 10 The solvated 4pti structure in VMD ou cccceeeeeseceeee
163. y another force field This situation is similar to combining force fields residues in the chemical system match templates in more than one of the specified force fields and all matching force fields are applied However in this case two or more force fields provide parameters for the same term for example two force fields provide parameters for the angle between atoms 1 2 and 3 causing a conflict The conflict is resolved by allowing the first force field that matches the residue to take precedence The order is the order in which the force fields were specified on the command line In all multiple force field assignment cases Viparr prints an error message and aborts if a bond exists between two residues that are not matched by the same force field The selected force fields should also have consistent van der Waals combining rules Otherwise Viparr will abort with an error message Viparr will print the following warning and error messages when matching residues to templates e If any residue matches more than one template in a force field then Viparr exits with an error No Viparr force field should contain identical templates e If any residue name is matched to a force field template with a different name a message is printed A maximum of 5 messages are printed per residue template name pair e Viparr will check that all residues are matched by one of the selected force fields If there are any unmatched residues Viparr wi
164. y are not identified as such in the cms file Viparr uses the atom ordering in the cms file and does not alter this ordering when creat ing the output file Residue numbering is also left unchanged and can begin with any integer including negative integers numbering does not even need to be contiguous which is typical to many PDB files Residues with different chain names can have the same residue number To aid in diagnosing problems with the input cms file messages involving residues have the form lt Chain_name residue_number gt xesidue_name and is usually preceded by a structure number CT number Viparr outputs a compressed force field representation when all the residues in a connec tion table are the same For a connection table that only contains water molecules this means that force field parameters are output only for a single water molecule For the 1su4 example used in Preparing a Desmond simulation with the System Builder on page 21 invocation of Viparr is very simple viparr py f charmm27 f spc 1su4_desmond cms 1su4_desmond_out cms where 1su4_desmond cms is the output file from the Desmond Panel The CHARMM 27 force field has built in parameters for the protein calcium and the POPC lipid model The resulting 1su4_desmond_out cms structure file along with the 1su4_desmond cfg config uration file that can be generated using the Applications gt Desmond gt Molecular Dynamics panel can now be used
165. y hydrogens ONone Polar only All Import and Process ls Review and Modify Refine Import structure into Workspace PDB Include diffraction data _ Biological unit ii Import Import structure file Browse Preprocess the Workspace structure Select these options j j Align to Selected entry PDB ___ T Assign bond orders Assign bond orders Add hydrogens Add hydrogens Remove original hydrogens Create disulfide bonds Create zero order bonds to metals Cap termini Create disulfide bonds Delete waters optional __ Convert selenomethionines to methionines Fill in missing side chains using Prime Fill in missing loops using Prime X Delete waters beyond 5 from het groups 7 Preprocess Click Preprocess T Perform the checked actions and fill out the tables in the Review Structure tab View Problems Protein Reports Ramachandran Plot Epik and Impact Glide are not installed L Reset Close Help 12 In the Preprocess the Workspace structure section select these options Assign bond orders Add hydrogens Create disulfide bonds The 4pti structure has three disulfide bonds which are all correctly recognized by the Protein Preparation Wizard Cap termini Select this option if you want the N or C termini capped There are many capping groups available the most common
166. yl row from the list of fragments The selected row is highlighted in yellow as shown in Figure 5 3 You can apply multiple mutants at a time by using CTRL click and SHIFT click to select the mutants from the Fragment Library When you select multiple fragments the FEP ligand mutation application creates different systems for each mutant and runs multiple thermodynamic cycles to compute respectively the binding free energy dif ference between the reference ligand and each of the selected mutants with respect to the receptor NOTE The short list of substitution groups is not a limitation it is a practical warning Any muta tion involving more than only a very few atoms is subject to very large uncertainty in the calculated Delta G values and it is virtually impossible to achieve converged results in a feasible simulation time Nonetheless you can create arbitrary groups rather than select ing mutations from the Fragment Library See Creating a Custom Fragment Group on page 71 for details 4 Click Start FEP simulation starts execution NOTE Desmond uses Bennett s acceptance ratio method for FEP calculations which means that numerous independent simulations will be run for a single FEP calculation Since the independent simulations can be run simultaneously you should be careful as to how April 2011 D E Shaw Research 65 Desmond Tutorial Preparing Free Energy Perturbation and Metadynamics many simulations can be allowed

Desmond Tutorial - DE Shaw Research

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