USER MANUAL M2 Mining Minima Software for Host
Contents
1. vent model Typically a complete analysis consists of successive execution of all processing tasks available under the Steps option on a loaded system The breakdown of the whole process into separate tasks allows the user to skip one or more tasks if desired and makes it possible for us to provide a set of GUI controls tailored for each task This chapter details the Steps options The Tools menu provides a number of additional capabilities to support the main M2 calculation These are explained in Chapter 6 5 1 Shared GUI components Several controls will always be provided in the left hand pane of the main M2 window irrespective of the chosen task These are the Load Run and Stop buttons along with the molecular graphics options At any step a struc ture to be studied can always be read into the program using the Load button which brings up a new window ti tled System Loading Figure 5 2 The Select a system type menu allows the user to load either a Single Molecule the host or guest or a Complex comprising both host and guest You will be prompted for topology TOP and initial co ordinate CRD files for each molecule to be loaded Note that for a complex two TOP and two CRD files are needed These files are loaded using the Load button of the System Loading dialog A trajectory file with additional conforma tions of the molecule or complex can also be loaded with the Load Trajectory button of the System Loading dialog2. System Loi xl Select a system type Single Molecule x Load Molecule Load Trajectory i Figure 5 2 Dialog box to load a single molecule or a complex as explained below Note that the trajectory file for a complex includes coordinates of both molecules even though M2 needs separate top and crd files for them In general clicking the Run button starts the calculation for the chosen Step and then loads the results into the GUI Clicking Run causes the GUI to gener 5 1 SHARED GUI COMPONENTS 19 ate an input file inp and to invoke the appropriate Fortran executable such as M2_1win exe This in turn reads the inp file and any needed molecular data files and carries out the calculation The results are written to files with out and or trj extensions where the out file provides information specific to the type of anal ysis selected from the Steps menu and the trj file provides Cartesian coordinates of any conformation s that were generated or selected by the run in a PDB style format The Stop button can be used to terminate the calculation without saving the results Note that the inp and molecular data files can also be copied to a Linux system and processed there by appropriately compiled versions of the chief M2 Fortran codes M2_1 exe energy minimization and Tork and M2_2 exe free energy calculations The lower section of the left pane of the main window provides options for the molecular graphics
3. e Display Each atom s name number type partial charge formal charge and vdW radius can be shown on the screen as can the distance angle and dihedral between any two three or four atoms respectively e For If Selected Atoms is displayed use the left mouse button to select atoms Alternatively use the pull down menu to choose all atoms Double click on the graphics background to deselect all atoms e In This pull down allows the display option to apply to the first loaded struc ture or all the existing structures e Conformation viewer Use the small arrows to step through conformations or enter the index of one or more conformations into the text window to display them or type in the text window to show all See the Tools menu for methods of computing RMSDs and superposing different conformations e Color By Color atoms according to the selected rules 20 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS 5 2 Energy minimization The initial window of M2 Figure 5 1 is by default in Minimization mode Mini mization mode can also be selected with the Steps menu Energy minimization is currently carried out in a two step process The first step uses the Conjugate Gra dient CG method and the second uses the truncated Newton TN method The CG method is better at handling the highly distorted conformations generated in the Tork procedure while TN is better at reaching a true local energy minimum The Parameters bu
4. Rotate a fo gd Kan gd c foo e Rotate torsion E to fpo gd I Show atom numbers Save Cancel Manual docking Figure 6 1 User interface for manual docking of guest into host binding site boxes below Rotate torsion hit Enter to visibly highlight the atoms and use the arrows or text box to change the angle 7 Repeat above procedures as desired 8 Finally click the Save button to write a trajectory file with the displayed coordinates of the complex e RMSD Once a set of conformations has been loaded into M2 this tool allows calculation of a simple root mean square deviation RMSD between any two conformations Upon selection of the RMSD option under the Tools menu the message Please select TWO structures to calculate the RMSD will appear The conformations should then be selected by typing their numbers into the Conformation viewer box their RMSD in A will appear near the top of the screen 34 CHAPTER 6 USER INTERFACE COMPONENTS TOOLS e RMSD by symmetry Same as RMSD except that the result will be corrected for molecular symmetries resulting in equal or lower RMSD values Superimpose Any number of loaded conformations can be superimposed with either of two methods principal axis and anchor atom The conformations to be superimposed are chosen by typing their numbers on the Conformation viewer box Selecting the Superimpose option under the Tools me
5. The PB Parameters and NP Parameters windows are shown in Figures 5 11 and 5 12 respectively and the GB parameters window is described above Note that the GB parameters used here must match those used in the free energy calculations or else the solvation energy correction will be done incorrectly The version of UHBD modified for use with M2 called m2uhbd automatically uses the maximal allocated finite difference grid dimensions It looks at the length x axis width y axis and height z axis of the molecule or complex and scales arectangular grid box to fit such that the molecule occupies 0 7 of each linear dimen sion of the grid See the UHBD manual http adrik bchs uh edu uhbd index html and publications 20 for details regarding the PB parameters In brief e Convergence Fractional convergence criterion for the finite difference solver e Ionic strength of solvent mM e Maximal number of iterations allowed in finite difference solver e Probe radius Radius A of solvent probe used to define dielectric boundary molecular surface e Radius of ions radius A of the dissolved ions making up the ion atmosphere otherwise known as thickness of the Stern Layer e Boundary cond 0 Zero boundary potential 1 Molecule is single DH sphere of radius 2 Sum of atoms as independent DH sphere default 3 Uniform applied electric field e Number of surface points number of points on each atom sphere used in defining the diele
6. imized and subjected to a thorough Tork conformational search The basic goal here is to put the guest into the host s binding cleft The procedure is as follows 1 use the Load system button to load Topology top and initial coordinate crd files for the ligand and receptor Make sure the Frame button is selected so that the docking box is vis ible and make sure the Box button is selected instead of the Ligand button so that the Translate and Rotate controls act on the box rather than the ligand Adjust the box size position and orientation so that it covers the targeted binding site of the receptor Click the Run Docking button and wait while the software builds a po tential grid in the docking box checks the energy of various positions and orientations of the ligand within the box and then displays the lowest energy conformation found If you want to further adjust the bound conformation click the Ligand button and use the Translate and Rotate controls to move the ligand around If you want to adjust a dihedral angle click Show atom numbers type the numbers of the 4 atoms defining the angle of interest into the text 32 33 Free Energy Calculation gt CH amp BS JI x Steps Tools Help Load system Run Docking Calculate energy Fame C Hidden Box size x afo ll y amo gd z dfo gd C Box Ligand Translate van gd Y foo gd z ad ell
7. number of requested distortion directions is large then a smaller tractable number of combined distortions is selected randomly 24 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS This parameter is the random number seed used in selecting the conformations Changing this seed is a way to generate a new Tork run that may turn up new local energy minima e Minimization type Minimization type where 1 refers to CG TN This option is just a place holder as no other types are available in this version of M2 e Use GB as the implicit solvent model uncheck to use vacuum The Other Parameters button provides access to the same energy minimization and energy parameters offered by the Parameters button in the Minimization step above 5 4 CONFORMATIONAL FILTERING 25 5 4 Conformational filtering Free Energy Calculation E 10 x Steps Tools Help Energy threshold 500 0 RMSD fos Angle tolerance 20 0 Keep all Hydrogens Ignore only C Hs Load Run Stop Calculation results Display atom Name xj For Selected Atoms xj In Displayed Structure xl Conformation viewer fi DI Color by Element el Center Conformation overlap checking and filtering Figure 5 7 User interface for conformational filtering The Filtering step Figure 5 7 uses a symmetry aware algorithm 5 to identify and delete duplicate and high energy conformations generated by the Tork search in
8. prompted with Load selected bonds window and the message A list of selected bonds exists for this structure Load them and if you click the OK button the list of selected bonds exists for CB structure will be loaded and you will see all the selected bonds highlighted These are the driver torsions mentioned above However if this is the CHAPTER 4 TUTORIAL A SAMPLE M2 CALCULATION first time running Tork on a new structure you will need to follow the next step in parentheses for selecting the key drivers e Choose the bonds that you believe need to be rotated as drivers by Tork in order to generate a good conformational search This is done by simply clicking on the bonds your selections will be highlighted To unselect all and start over double click on the background of the graph ics window Completing this process causes the M2 GUI to write two additional files to disk so that your selections will be saved and available for subsequent calculations These two files have bondlist out and fingerPrint out extensions and here are named CB bondlist out and CB fingerPrint out e Click on the Tork Parameters button and the Parameters for Tork win dow will open The default values for the Tork conformational search parameters appear and may be changed if you wish GB is selected as the solvation method by default and can be removed by un checking the corresponding box at the bottom section of the window Then click OK The Other Para
9. 22 0 win32 py2 2 exe OpenGL_2 0 1 03_install rar 3 2 INSTALLATION OF THIRD PARTY PACKAGES 7 e plink exe e Pmw 1 1 tar gz e PmwBlt py e psftp exe e Python 2 2 2 exe e win32al1 148 exe In order to extract some of the third party software extensions you will need extrac tion utilities that can extract zip files as well as tar and tar gz files Such soft ware can be found on line http www winzip com and http www rarlab com download htm for example 1 Double click on the Python 2 2 2 exe icon and follow all accompanying in stallation instructions to install Python 2 2 2 MAKE SURE TO NOT USE ANY OTHER VERSION OF PYTHON While you may not choose to install all of the components of Python 2 2 2 you must install the Python interpreter and libraries the Tcl Tk components and the Python utility scripts Note the default repository directory c Python22 is acceptable 2 Install all win32 extensions for Python 2 2 2 by double clicking the win32a11 148 exe icon and following all accompanying installation instructions 3 Install the Numeric extensions for Python 2 2 2 by double clicking the Numeric 22 0 win32 py2 2 exe icon and following all accompanying instal lation instructions 4 Double click the bsddb3 3 4 0 win32 py2 2 exe icon and follow all accom panying installation instructions to install the BSD database extension 5 Using an appropriate extraction utility open the Pmw 1 1 tar gz file Extract the file
10. 5 4 Dialog box to set Generalized Born parameters 21 5 5 User interface for the Tork conformational search step 22 5 6 Dialog box to set Tork conformational search parameters 22 5 7 User interface for conformational filtering 25 5 8 User interface for free energy calculation step 2 27 5 9 Dialog box to set parameters for free energy calculation step 27 5 10 User interface to correct free energies with PB SA solvation model 29 5 11 Dialog box to set parameters for Poisson Boltzmann solvation calculations 29 5 12 Dialog box to set parameters for nonpolar solvation component 30 6 1 User interface for manual docking of guest into host binding site 33 ill Chapter 1 Introduction The second generation version of Mining Minima M2 provides a systematic method for calculating the binding affinities of host guest systems by computing the standard chemical potentials of the free host the free guest and their complex and taking the difference to obtain the standard free energy of binding M2 relies on the predominant states approximation 1 2 to estimate the configuration integral of a molecule or complex as a sum of contributions from its local energy minima i e its low energy conformations The potential energies of the host and guest are estimated with an empirical force field In order to reduce the number of degrees of freedom and hen
11. A implies the difference between the complex and free species The 3 RT correction usually is small in relation to the other quantities and is often neglected 2 6 AU W A 3RT The estimated change in mean energy provided by Equation 2 6 can be com bined with the change in binding free energy to yield the change in configurational entropy 7 which accounts for changes in the mobility of the host and guest on binding AS o config 2 7 T AS tig AC A U W It is important to be aware that the change in configurational entropy includes changes in the rotational translational conformational and vibrational entropy of the host and guest molecules upon binding but it does not include the change in solvent entropy The change in mean energy on binding can also be decomposed into Boltzmann averaged terms plus the equipartition contribution 2 8 A U W A U yaw AU Gout AU vat A Wetec SE A Wnp Se Eeq representing respectively the changes in mean van der Waals energy Coulombic energy valence energy comprising bond stretches angle bends and dihedral rota tions electrostatic solvation free energy from the PB model nonpolar solvation free energy from the surface area based approximation and the equipartion contribution The change in van der Waals energy for example is computed as els zi Uvaw i 2 9 Maw SCH S where Uaw is the van der Waals energy at the local energy minimu
12. PB and NP terms It is a good idea to use the same GB parameters in this Free Energy Correction step as in the prior steps e Click Run and you will be prompted to load the file of free energies ob tained in previous step CR fe out The calculation then generates sev eral intermediate output files CB_fe gb out CB_fe np out and CB_fe pb out which include respectively the bond angle dihedral improper vdW Coulombic Generalized Born GB Non Polar Cavity NP and Poisson Boltzmann PB solvation energies of the filtered conformations You will also see a file whose name ends new final out here CB_filter new final out which has all the energy components of the individual conformations and ends with a summary of overall average energy entropy and free energy 7 Repeat the steps described above for the guest B5 and B5complex CB B5 cases and you will have the corresponding output and trajectory files The fi nal free energy and Boltzmann averaged energy components for all the 3 cases CB B5 and B5complex can be found on the last block of CB_filter new final out B5 filter new final out and B5complex filter new final out files To obtain the binding free energy changes in the mean potential plus solvation energy A U W and changes in Boltzmann averaged energy components you need to subtract the corresponding values for the host and guest cases from the complex values Given the usual standard concentration of 1 mol li
13. STEM VARIABLES found near the bottom Click the EDIT button Scroll to the end of the line and add c Python22 without the quota tion marks Click OKAY three times to close the SYSTEM window Close the CONTROL PANEL window At this point the installation of required third party software is complete 3 3 Installation of M2 codes This final section provides instructions for installing the Mining Minima version 2 A 2 software The following files should be included with this distribution of Mining Minima version 2 A 2 If any or all of these programs are missing please contact the Gilson Group for replacement copies The provided directory M2_FILES contains the following files and directories e figures dir mnlogo gif title_umda gif 3 3 INSTALLATION OF M2 CODES 9 e parameters dir atomTypes dat bonds dat angles dat dihedrals dat impropers dat LJones dat e Python Files freeEnergy pyc getAngParam pyc getAtParam pyc getBondParam pyc getDihedParam pyc getImpropParam pyc getPSFAtType pyc M2 py numeric_tools pyc numericTools pyc order pyc ProgressBar pyc psf2top pyc ssh pyc telnet pyc togl_opengl1_1 pyc t t t t t t 4 toolBox pyc e Executable Files calrmsd exe Executable to calculate RMSD between conformations chkconfic win exe Executable to filter duplicate conformations Note that the maximum number of bonds to a single atom can not exceed 8 bond
14. USER MANUAL M2 Mining Minima Software for Host Guest Binding Version 2 A 2 beta Sarvin Moghaddam moghaddam umbi umd edu and Michael K Gilson gilson umbi umd edu Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute Rockville MD 20850 University of Maryland Biotechnology Institute August 24 2009 Contents Contents 1 Introduction 2 Overview 3 Installation 3 1 System preparation 4 64 ee 64 a bo Ew neh Ewe ere eV EES 3 2 Installation of third party packages 00 3 3 Installation of M2 codes lt lt 4 lt 4 ee be dk DASE YE CES 4 Tutorial A Sample M2 Calculation 4 1 Procedure A ss mtos eura koiaaa HSA ww Gere Wa e See A 5 User Interface Components M2 Steps 5 1 Shared GUI components 5 2 Energy minimization lt lt 4h 6444 648 eed de eee SE A 5 3 Tork conformational search 5 4 Conformational filtering e a ed eee koa a bE eee ESS 8 5 5 Free energy calculation 5 6 Free energy correction 2 4 45 4 45 EEN EE De eee Se 6 User Interface Components Tools 7 M2 Files Contents and Format 11 11 17 18 20 22 25 27 29 32 36 ii CONTENTS 8 Compilation and Automation 38 9 Tips and Troubleshooting 40 List of Figures 5 1 Main M2 window with cucurbituril guest complex ke 5 2 Dialog box to load a single molecule or a complex 18 5 3 Dialog box to set energy minimization parameters 21
15. aded now via the Load Trajectory option provided in the Sys tem Loading window The second way is to use Manual Docking method available in the Tools menu Note however the docking tool is far from a polished product Either way once a suitable starting conformation is loaded for the complex the minimization can proceed In the present example we used the Manual Docking to generate the conformation in B5complex_ManualDocking trj This file should now be loaded with the Load Trajectory option 3 Conformational search with the Tork algorithm Normal mode analysis in Bond Angle Torsion coordinates is used to define natural distortions of the molecule or complex These are projected onto a key subset of torsional coordinates drivers selected by the user Cycles of distortion and energy minimization are used to discover new local energy minima e Select the Tork option under the Steps menu and the Tork window will open For simplicity here we present instructions for the CB host but corresponding files for the B5 guest and the complex cases can be find in the Sample folder e If you just energy minimized a molecule or complex above it is already loaded and available for this next step If not start by loading your molecule and energy minimized trajectory by using the Load button as above If you are working on the tutorial and you have the CB trj conformation loaded in you system then as soon as you select the Tork option you will be
16. be done by modifying the file parameters inc maxatm maximum number of atoms maxbnd maximum number of bonds maxang maximum number of angles maxdih maximum number of dihedrals maxnb maximum size of the nonbonded pairlist e The default compilation settings only need to be supplemented with the flags fpp to enable preprocessing and stack 0xldcd6500 to increase the stack size e To port the code to the Linux environment and compile with the Intel ifort compiler 38 39 Place all the source code files provided in the VisualFortranWindows sic folder in a single directory on the Linux system along with the provided Makefile Type make all at the Linux prompt to build the program M2_1 exe and M2_2 exe should be run at the command prompt with the names of the desired input and output files on the command line e g M2_1 exe B5 tork tork inp B5_tork tork out You may use the input files generated with the Windows GUI as models for your Linux runs The Scripts folder provided with this distribution includes a collection of an cillary scripts that automate the process of iterating the Tork free energy calculation cycle to convergence Please refer to the ReadMe file in the Scripts folder for information Chapter 9 Tips and Troubleshooting e If the graphics window does not display a molecular system when you first load it use the right mouse button to rescale the display and the molecu
17. by Element xl Center Free energy calculation 27 Figure 5 8 User interface for free energy calculation step 5 5 Free energy calculation In the Free Energy step each of the filtered set of conformations above are processed with the HA MS method Chapter 2 to provide an estimate of its free energy chemical potential The result ing free energies are also combined to provide the full free energy of the molecule or complex The calculation will process whatever conformations are currently loaded into the M2 GUI These might have just been selected in the Filtering step above Al ternatively the user can load a trj file with con formations to be processed The interface for the Free Energy step Fig Number of lowest Ta modes to scan Temperature 300 Number of minima fi Sampling width in fo std dev e Minimization type fi EE intest value p2 IV Use GB as the implicit solvent model f j Figure 5 9 Dialog box to set parameters for free energy cal culation step ure 5 8 provides access to many of the same parameters that appear in other M2 steps as described above choosing the FE Parameters button provides access to the 28 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS parameters unique to the free energy step through the Parameters for Free Energy window Figure 5 9 as e Number of minima Number of filtered conformations to be processed w
18. c cavity radii in which the van der Waals radius of the atom was averaged with the probe radius 5 2 ENERGY MINIMIZATION 21 Figure 5 3 Dialog box to set energy minimiza tion parameters Note that the energy minimiza tion will process whatever structure is currently loaded If no structure is loaded you will need to load one as described above If only a top and crd file are read in then the starting conformation will be that in the crd file However a different initial con formation can optionally be read in from a trj file above Note that although providing an initial trajec tory file is optional if the confor mation in the crd file is pathologi cal minimization may yield a strained and unrealistic conformation Figure 5 4 Dialog box to set Generalized Born parameters 22 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS 5 3 Tork conformational search Free Energy Calculation Steps Tools Help Tork Parameters Other Parameters Select rotatable bonds Me i Run Stop Calculation Progress om Name For Selected Atoms xj In First Structure sl Conformation viewer EIN E Color by Element sl Center Tork conformation search Figure 5 5 User interface for the Tork conformational search step Selection of the Tork option under the Steps menu will change the menu on the left pane of the main window to that in Figure 5 5 By default the To
19. ce of local energy minima the solvation free energy is estimated with an implicit solvent model The free energy of each energy well is estimated with the harmonic approximation HA adjusted for potential anharmonicities by the Mode Scanning approach 3 Chapter 2 of this manual summarizes the theory underlying the method Chap ter 3 presents the instructions for installing the components required for running M2 Chapter 4 goes through the steps for computing the binding affinity of a host guest system with sample files provided along with the software Chapters 5 and 6 provide greater detail regarding the user interface components of the M2 software Chap ter 8 provides detailed information about compiling the source code and Chapter 9 provides tips for avoiding pitfalls and getting meaningful results from M2 calcula tions Chapter 2 Overview The M2 method computes the free energy of host guest binding as 2 1 ACHT ee host 9 ae where eomplex Hhost ANd Hguest are the standard chemical potentials of the com plex host and guest molecules respectively The standard chemical potential of a molecule in solution is approximated as a sum over M local energy minima 8r M 2 2 u RT In ES RTIn zx where 2 3 a petra and R T C E r and z are respectively the gas constant the absolute tempera ture the standard concentration the energy as a function of the internal coordinates r and the configuration int
20. ck the Return to M2 button and you will be back in the main M2 window Repeat procedure for the guest starting with file B5 psf 2 Energy minimize the starting conformations and write the outputs to trj files This step is done because M2 needs to start from a local energy minimum Select Minimization under the Steps menu option which is the default starting window of the M2 Click the Load button and the System Loading window will appear on the screen Click Load Molecule Leave the pull down menu on Single Molecule You are prompted to browse for the TOP and CRD files of CB molecule sequentially Click on the Parameters button and the Minimization Parameters win dow will open The default values for the minimization parameters appear on the top section of the window These values can be used without any change or may optionally be changed by the user The user is also al lowed to choose which components of the vacuum energy will be taken into account where by default all the energy components are selected GB is selected by default as the solvation method but the user may des elect the GB option by un checking the corresponding box at the bottom section of the window in which case no solvation model will be used If GB is selected the user may click on the GB Parameters button and the Parameters for GB Solvation window will open Again there are some default values assigned for the GB calculation unless the user pref
21. ctric boundary molecular surface Default 500 The nonpolar surface energy is estimated as Wnp C1 A Co where A is the solvent accessible Ditze xj surface area and C and Ch are empirical parame ters based on experimental solvation data The NP CONAMA E Parameters window allows the following parameters Coefficient ba to be set l i Intercept 0 0 Number of points 500 OK Cancel Figure 5 12 Dialog box to set parameters for nonpolar solva tion component e Solvent radius Solvent probe radius A used in computing solvent accessible surface area 5 6 FREE ENERGY CORRECTION 31 e Coefficient Coefficient for surface energy Ci default 0 006 keal mol A e Intercept Intercept for surface energy Co de fault 0 kcal mol e Number of points Number of points per atomic sphere used in the numerical calcula tion of the surface area default 500 Clicking the Run button causes the GUI to ask for the name of a free energy file from the Free Energy step above which must correspond to the loaded conformations It will output a file with new final out extension with the corrected free energies Chapter 6 User Interface Components Tools The Tools menu provides access to a number of tools that support execution and analysis of M2 results e Manual Docking This tool Figure 6 1 is designed to help set up a reasonable initial conformation of a host guest complex which will then be energy min
22. e CRD and TOP files in the Sample folder Neither of the files should contain any header title at the beginning or any other comment in between or at the end of the files It is important that the pathnames associated with the M2 repository or any of your working directories do not contain any blank space character or be too long When you generate a TOP file using the Make TOP File option under the Tools menu check that all the parameters are defined and your TOP file does not include any n a flags This flag if present means that a parameter required by the PSF file is not present in the parameter data files You will need to provide such parameters yourself by manually editing the TOP file For example the NX CT NX angle set is not defined in our CB original top file see Sample folder and a reasonable value has been manually inserted in CB top Bibliography 12 is Gilson M K Prot Struct Func Gen 1993 15 266 282 Gilson M K Given J A Head M S Chem amp Biol 1997 4 87 92 Chang C E Potter M J Gilson M K J Phys Chem B 2003 107 1048 1055 Chang C E Gilson M K J Comput Chem 2003 24 1987 1998 Chen W Huang J Gilson M K J Chem Inf Comput Sci 2004 44 1301 1313 Kolossvary I J Phys Chem A 1997 101 9900 9905 Chang C E Chen W Gilson M K Proc Natl Acad Sci USA 2007 104 1534 1539 Head M S Giv
23. e sure they are appropriate and that you match them as closely as possible For example if the experiments use cyclodextrins at high concentration then the binding measurements may reflect not only 1 1 host guest binding but also the formation of higher order complexes such as a 2 1 cyclodextrin guest complex Or if the solvent is a mixture of water and methanol it may be hard to settle on appropriate solvation parameters for use in M2 In order to avoid file format problems it is safest to generate all input files via the M2 GUI You can use a text editor to revise them but be sure to maintain an identical format Remember to add the contribution of RT In sr 7 03 kcal mol to the computed binding free energy See Equation 2 2 and Section 4 1 Filtering may crash when there is a large number of conformations If this happens divide the trj file into several separate trj files with fewer conforma tions filter them separately merge the filtered files and then filter the merged file to get the final filtered trj file 42 CHAPTER 9 TIPS AND TROUBLESHOOTING Remember that the present conformational filtering program will fail if an atom has more than 8 bonds This can happen in the case of some metalloor ganic complexes You have the option of using a third party filtering program and then loading the filtered conformations back into M2 for the free energy calculations CRD and TOP files should follow the same format as th
24. egral over internal coordinates in energy well i Factors that will cancel in the final free energy difference have been omitted Local energy minima are identified with the Tork search algorithm 4 carried out by executable M2 1win exe or M2_1 exe and local configuration integrals are computed with the Harmonic Approximation Mode Scanning HA MS method 3 M2_2win exe or M2_2 exe Because the Tork search can arrive at the same conformation more than once duplicate conformations are eliminated with a symmetry aware algorithm to prevent double counting 5 chkconfic win exe or chkconf1c win exe For a molecule or complex with N atoms the HA MS method works by di agonalizing the Cartesian Hessian matrix of the energy at a local energy minimum to obtain 3N 6 Cartesian modes each comprising an eigenvalue and an eigen vector The modes can then be used to approximate the Boltzmann distribution in the energy well as a multidimensional Gaussian with principal axes equal to the eigenvectors and standard deviations along these axes directly related to the corre sponding eigenvalues The free energy of the well is then estimated as sum of 3N 6 contributions from the respective modes 3 The software starts by projecting the eigenvectors onto Bond Angle Torsion coordinates 3 It then estimates the free en ergy of the well by integrating the Boltzmann distribution along each mode limiting the domain of the integral to the lesser of 3 s
25. en J A Gilson M K J Phys Chem 1997 101 1609 1618 Polar hydrogen parameter set for CHARMm Molecular Simulations Inc Waltham MA Brooks B R Bruccoleri R E Olafson B D States D J Swaminathan S Karplus M J Comput Chem 1983 4 187 217 MacKerell A Bashford D Bellott M Dunbrack R Evanseck J Field M Fischer S Gao J Guo H Ha S Joseph McCarthy D Kuchnir L Kuczera K Lau H Mattos C Michnick S Ngo T Nguyen D Prodhom B Reiher W Roux B Schlenkrich M Smith J Stote R Straub J Watanabe M Widrkiewicz Kuczera J Yin D Karplus M J Phys Chem B 1998 102 3586 3616 MacKerell A D Jr Widkiewicz Kuczera J Karplus M J Am Chem Soc 1995 117 11946 11975 43 44 13 14 15 16 17 18 19 20 21 22 23 BIBLIOGRAPHY Weiner S J Kollman P A Case D A Singh U C Ghio C Alagona G Profeta S Weiner P J Am Chem Soc 1984 106 765 784 Cornell W D Cieplak P Bayly C I Kollman P A J Am Chem Soc 1993 115 9620 9631 Gilson M K Honig B J Comput Aided Mol Des 1991 5 5 20 Qiu D Shenkin P S Hollinger F P Still W C J Phys Chem 1997 101 3005 3014 Gilson M K Honig B Prot Struct Func Gen 1988 4 7 18 Sitkoff D Sharp K A Honig B J Phys Chem 1994 98 1978 1988 Chang C E Gilson M K J A
26. ers to revise them Click OK and you will return to Minimization Parameters window Click OK in the Minimization Parameters window Click the Run button and the Save Trajectory window will open Enter a name in the File name box and click the Save button For simplicity let s call the file CB trj Click the Run button The GUI will write input file CB em inp to disk and will invoke M2_1win exe to carry out the minimization specified in this input file The calculation will generate file CB trj containing the energy minimized conformation and CB em out which is the log of the run See Section 7 for details regarding these files 4 1 PROCEDURE 13 e Repeat the same procedure to energy minimize the guest molecule start ing with B5 psf to generate files B5 em inp B5 em out and B5 trj in your folder e For the CB B5 complex B5complex after clicking the Load button in the Minimization window use the pull down to select the Complex op tion under the Select a system type and you will be prompted to load the TOP and CRD files of CB using Load Host button and B5 us ing Load Guest button sequentially You will see that the guest lies outside the host and we need a starting conformation with the guest at least approximately docked into the host You can address this in one of two ways The first way is to generate a suitable starting conformation with a separate program and write it as a PDB format trj file this can be lo
27. file which holds Cartesian coordinates of the output conformations in a stacked PDB format For further information on this format please see the source code that generates it wtrjlm_new f 36 5 ER inp An input file written by the GUI for one of the M2 executables The lines should be reasonable self explanatory based on the parameters visible in the GUI windows and discussed in this manual out An output file from one of the M2 steps The final output file new final out contains the chemical potential free energy and energy components for all the filtered and sorted conformations along with the corresponding cumulative results Chapter 8 Compilation and Automation The source code for M2_1win exe and M2_2win exe is provided in the files M2_1 zip and M2_2 zip respectively The code is written in FORTRAN 90 and was devel oped and compiled on Windows XP with Compaq Visual Fortran We have also successfully compiled both executables with the Intel R Fortran compiler under the Windows XP and Linux operating systems The IntelWindows and VisualFor tranWindows folders contain the source code and workspaces for the corresponding compilers You may need to modify the paths in the workspaces to match your usage in order to use these The following notes provide additional information for compiling and running the M2 codes e If you work on a large system you may need to increase the sizes of some arrays This can
28. ifferent random number 40 Al seeds The present default parameters are based on our experiences with the M2 software but it is not a bad idea to experiment with variations if only to get a sense for what they all do Occasionally Tork will not fully energy minimize a conformation In this case the Mode Scan that occurs during the HA MS free energy calculation may scan into a lower energy conformation The way this plays out in the math is that the conformation in question will be reported to have an abnormally large favorable entropy Therefore if you come across a conformation with a surprisingly large entropy it is a good idea to try re minimizing the energy and recalculating its free energy just to be sure it is all right The code does try to catch these problems in advance if the energy decreases more than mintest during Mode Scanning Section 5 5 the scan is terminated and a warning message is written to the console The version of UHBD that we adapted for M2 automatically scales the finite difference grid to fit the molecule or complex you are studying However if your system is too large the finite difference grid spacing may become too coarse to yield good PB results A grid spacing of 0 3 Angstroms or smaller is best It is a good idea to check _fe pb out to make sure that UHBD is using a sufficiently fine grid When comparing with experiment always take a careful look at the experi mental methods to mak
29. ith HA MS calculations e Number of lowest modes to scan Number of modes with low force constants to be scanned for anharmonicity and integrated numerically if they prove suf ficiently anharmonic see Chapter 4 1 All remaining modes will be treated harmonically e Minimization type Minimization type where 1 refers to CG TN There are no other types available in this version of M2 e Temperature Temperature in Kelvin e Sampling width in std dev Each mode will be integrated either by HA or MS out to the lesser of this number of standard deviations and a 60 change of any torsion angle e Mintest value kcal mol Occasionally mode scanning along a mode yields an energy lower than that of the initial nominal energy minimum This im plies that the starting conformation was not fully energy minimized and this condition can lead to large errors in the M2 results If the energy changes by more than this tolerance during mode scanning the scan is terminated and a warning is output e Use GB as the implicit solvent model GB is used by default Clicking the Run button causes the GUI to ask for a name for the output file then generates an input file for M2 2win exe and invokes this program to process the conformations The results are displayed in the Calculation Results box in the left hand pane of the GUI and also in the selected output file 5 6 FREE ENERGY CORRECTION Free Energy Calculation Steps Tools Help PB Para
30. k trj e The default values for the conformation overlap checking and filtering are shown and can be modified in the main Filtering window See Sec tion 5 4 e Click Run and you are prompted to enter a name for the filtered trajectory file for example CB filter tri e When the filtering process is finished the number of conformations will have decreased because duplicates will have been removed As before the file CB_filter opt inp includes the input parameters to the filter ing algorithm and file CB_filter opt out is the output log file The file CB_filter trj includes the Cartesian coordinates of the filtered confor mations in PDB format 5 Calculate the chemical potentials and overall free energy of the filtered con formations e Select Free Energy under the Steps menu option and the Free Energy window will open e If you just finished the Filtering step above the filtered trajectory should already be loaded and available for the free energy calculations Otherwise load your structure top and crd and your filtered confor mations trj with the Load button as above e The FE Parameters show the default parameters for use in free energy calculations Automatically the Number of minima box should show the number of filtered conformations The Number of modes by quadrature may be adjusted by the user but it defaults to 10 based on our experience This means that the 10 modes with the lowest eigenvalues will be scan
31. le s should show up e Starting with a poor conformation can lead to trouble In particular make sure that the initial bound conformation of your complex looks basically reasonable Be aware that a conformation can be energy minimized to a local energy minimum yet be incorrect due for example to damaged stereochemistry a covalent bond thrust through a phenyl ring a ligand outside the receptor etc e Tork is an aggressive search algorithm and sometimes generates abnormal con formations especially of macrocyclic hosts Be sure to view the conformations before computing the free energy If there are abnormal conformations you can simply use a text editor to excise them from the trj file to be used in the free energy calculations e If the Tork calculations for the bound complex generate conformations with the guest outside the binding site it is usually a good idea to delete these conformations before proceeding e Be aware that the free energy results depend upon the force field you use Whereas the force field parameters for amino acids have been pretty highly optimized over the years this is not the case for the varied atom types that appear in host guest chemistry If your results are unsatisfactory it is a good idea to take a critical look at the force field parameters or try using a different set e Especially when working with a new system it is a good idea to get a sense for the convergence by doing several Tork runs with d
32. llowing the steps below you can build the necessary files to load your molecule 1 Use QUANTA Accelrys San Diego CA to generate psf Protein Structure File and crd files Choose Tools in the main M2 window Select Make TOP file Select Convert PSF Use the Browse button to select the Quanta psf file oh abe te i 35 6 The top file name should appear automatically in the same location with the same name as the psf file except with the top extension However you may change the name or location here 7 Press the Convert button This will generate the files 8 Select the Return to M2 button and you will have the corresponding TOP file e TRJ CRD This allows a CHARMM format crd file to be generated from a conformation displayed in the M2 graphics window e CRD TRJ Reverse of the previous option e Link files Allows multiple trj files to be linked into a single trj file This can be useful for example when multiple Tork outputs need to be combined into a single trj file for conformational filtering Note that M2 does not allow multiple trj files to be loaded at the same time so linking them before loading is the only option Save target file allows the user to specify the desired name of the output trj file Then the File Selection Dialog allows the user to choose the trj files to be linked Once the output trj file has been written it can be loaded with the Load button for further work e E
33. m Chem Soc 2004 126 13156 13164 Davis M E Madura J D Luty B A McCammon J A Comput Phys Commun 1991 62 187 197 Zhou H Gilson M K Chem Rev 2009 Articles ASAP July 9 2009 Chen W Huang J Gilson M K J Chem Inf Sci 2004 44 1301 1313 Gilson M K Gilson H S R Potter M J J Chem Inf Comput Sci 2003 43 1982 1997
34. m 2 For a full M2 calculation we recommend carrying out multiple iterative cycles of Tork search and HA MS free energy calculations where each successive cycle starts with the most stable conformations found so far and continuing this process until the cumulative free energy stabilizes Sample scripts for carrying out this process under Linux are included with the present distribution see Chapter 9 Chapter 3 Installation This section contains instructions for installing the components required for running Mining Minima on a computer with the Windows XP Professional operating system The installation is divided into three parts 3 1 System preparation You should be logged in with administrator permissions Before continuing with the current installation please be sure to uninstall any Python related software using the ADD REMOVE PROGRAMS function found under CONTROL PANEL Mining Minima version 2 A 2 may not perform properly if the required versions of third party software including Python and Python related software are not installed 3 2 Installation of third party packages The following third party software packages should be included with this distribution of Mining Minima version 2 A 2 If any or all of these programs are missing please contact the Gilson Group for replacement copies The directory THIRD PARTY should contain the following files e blt 4u for 8 3 exe e bsddb3 3 4 0 win32 py2 2 exe glut32 dll e Numeric
35. meters NP Parameters GB Parameters Load Run Stop Calculation Results Display atom Name sl For Selected Atoms sl In Displayed Structure xj Conformation viewer af d Color by Element Ka Free energy correction 29 iol x Figure 5 10 User interface to correct free energies with PB SA solvation model 5 6 Free energy correction The final step Free Energy Correction involves adjusting the free energies from the HA MS method by subtracting out the GB solvation en ergy computed at the base of each energy well and adding back the solvation energy computed with the PB SA solvation model This esti mates the solvation free energy as an electrostatic part computed with the PB continuum model and a nonpolar part estimated as proportional to molecular surface area with an empirical coeff cient PB Parameters SST E Probe radius 1 4 Convergence In om Radius of ions Joo lonic strength foc Boundary cond 2 Mottertones 1 00 Number of Ee of iterations ui ol surface point 500 Number of minima fi Center the grid on the selected atoms I Apply deielectric boundary smoothing Figure 5 11 Dialog box to set parameters for Poisson Boltzmann solvation calcula tions 30 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS The M2 interface for this step Figure 5 10 pro vides access to the parameters of the GB PB and NP solvation terms via the corresponding buttons
36. meters button provides access to the same set of parameters as in the Minimization step above e Click the Run button e You are prompted to enter the name of an output trj file to store the conformations found by Tork Here call it CB_tork trj and click Save e After the job is finished you will have additional input and output files in your folder Here CB_tork tork inp is the input file read by M2 1win exe and CB_tork tork out and CB_tork trj are the log and conformational trajectory files The conformational trajectory file in cludes the Cartesian coordinates of all the conformations generated by the Tork search in PDB format You will also be able to choose and view the various conformations by using the small left and right arrows under the Conformation viewer box or by typing in the desired conformation numbers into the text box Note that the conformations are sorted by their potential energy where the first conformation has the lowest poten tial energy and so forth 4 Remove duplicate conformations filtering e Select Filtering option under the Steps menu option and the Filtering window will open e The trajectory obtained in the prior Tork step should be available at this point unless you closed and reopened the GUI before this step In this case load the Tork trajectory output file by choosing the Load button and 4 1 PROCEDURE 15 choosing the CB crd CB top files and also the Tork trajectory output file CB_tor
37. ned and potentially corrected for anharmonicity while all higher modes will be treated harmonically e The Other Parameters button provides access to the same set of param eters as in the Minimization and Tork steps e Click Run and you will be prompted for the name of an output file e g CB fe out After the calculation is finished you will have CB_fe im inp which includes the input parameters read by M2_2win exe and the CB_fe out output file includes the free energy of the filtered conformations 6 Adjust the solvation free energies This step involves reading in the filtered trajectory file a second time computing the Poisson Boltzmann PB surface area nonpolar NP solvation free energy for each conformation and using this to adjust the free energies of the minima computed in the prior step CHAPTER 4 TUTORIAL A SAMPLE M2 CALCULATION e Select the Free Energy Correction option under the Steps menu option and the Free Energy Correction window will open e If you just calculated the free energy of the conformations obtained fol lowing the Filtering step the structures are loaded and available for this step If not start by loading your structures by using the Load button as above e PB Parameters and NP Parameters windows show the default parameters for use in PB and NP calculations GB Parameters are also shown because the correction step requires computing and subtracting off the GB solvation energy before adding the
38. nu brings up the Superposition method selection box which allows the desired method to be chosen Clicking the OK button causes the superposition to be carried out The principal axes method compute the center of mass and principal moments of inertia of each molecule and aligns them The anchor atom method translates and rotates the molecules to optimally superimpose the selected atoms De superimpose Undoes a conformational superposition above Read MDL Reads in the chemical structure of a molecule in MDL Molfile format in order to enable calculation of partial atomic charges below Partial Charges If the Vcharge program 23 has been obtained from Ver aChem by the user free for noncommercial use at www verachem com this command allows calculation of Vcharge conformation independent ab initio like partial atomic charges for an MDL Molfile Once the Molfile is loaded above choose the Partial Charge option under the Tools menu to bring up the Partial Charge window and click Run button The charges will be calcu lated and written into a new file with extension _vcharge mol The Calculate and Smooth options here are briefly described in the tooltips visible by hov ering the mouse over these buttons If desired the user can manually replace the existing charges in a TOP file with the new charges generated via Vcharge Make TOP file Allows a top file with Quanta CHARMm parameters to be generated from a Quanta psf file Fo
39. o carry out a one cycle M2 calculation for a sample host guest system A full calculation should normally include multiple cycles as noted at the end of Chapter 2 This involves calculating the chemical potential of the free host the free guest and their bound complex and taking the difference to obtain the standard free energy of binding 4 1 God HB5complex HOB _ HB5 The example provided with this software consists of cucurbit 7 uril CB and 1 4 bis methylamine bicyclo 2 2 2 octane B5 A single cycle of M2 calculation yields a binding free energy of about 22 kcal mol All the required input files can be found in the Sample folder provided with this software distribution Section 7 describes the various input and output files resulting from this process 4 1 Procedure 1 Prepare the molecules Here you will read in a psf file generated by the program Quanta Accelrys San Diego CA for each molecule assign force field parameters to it and save the resulting topology top file for future use e Run M2 by double clicking M2 pyc in the corresponding folder e From the Tools menu select Make TOP file e Choose PSF Converter then browse for and open file CB psf 11 12 CHAPTER 4 TUTORIAL A SAMPLE M2 CALCULATION By default the filename CB top should appear in the box labeled Input the name of the Topology file to be written Click the Convert button and after the execution which should be very quick cli
40. order to avoid overcounting any conformations in the subsequent free energy cal culations Note that the current filtering code fails if any atom has more than 8 bonds Key parameters for filtering are the Energy threshold Angle tolerance and RMSD whose default values are 100 kcal mol 15 0 degrees and 0 1A respectively The filter deletes all conformations whose energy after Tork search is above the energy threshold relative to the lowest energy conformation found The angle tol erance is a criterion needed for the identification of 3 dimensional symmetries 22 For every pair of conformations whose symmetry corrected RMSD is less than the RMSD limit the higher energy conformation will be deleted By default only po lar hydrogens are included in this symmetry based conformational filtering because discarding nonpolar hydrogens saves computer time and does not appear to degrade 26 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS the results Nonetheless the option is provided to include all hydrogens Clicking the Run button causes the interface to prompt for the name of an output trj file which will contain the coordinates of the conformations that survive the filtering step 5 5 FREE ENERGY CALCULATION Steps Tools Help FE Parameters Other Parameters Load Output Run Stop E Calculation Progress Calculation Results Display atom Name sl Fo Selected Atoms sl ees Conformation viewer E Color
41. procedure as follows e Energy threshold kcal mol A Tork distortion continues until the energy rises above this threshold relative to the starting conformation then energy minimization begins e Number of probes Number of different initial local energy minima from which a Tork search will be initiated e Number of energy thresholds If value is greater than 1 then the Tork dis tortion will continue past the first crossing of the energy threshold until the desired number of multiples has been passed a new minimization will be started at each crossing e Torsion angle for overlap checking two conformations generated by Tork are considered distinct if any of their freely rotating dihedrals differ by more than this value Eliminating repeat conformations in this way during the Tork search reduces the amount of redundant searching e Number of steps Maximum number of distortion steps along each distortion mode e Energy cutoff kcal mol When the rise in potential energy exceeds this value the search will stop e Step size Size of each small distortion step e Sampling type Tork distortions can be carried out along single pure distortion modes along with random combinations of pairs of modes Type 1 or random combinations of pairs of modes only Type 2 You may want to vary these heuristic options in a series of Tork searches to make sure you find the very lowest energy conformations possible e Random seed If the total
42. rk search step uses whatever molecular conformation is already loaded as starting point for its conformational search However the user can load other conformations in the form of a trajectory file and the Tork algorithm uses all conformations that are loaded as starting points The Tork method involves re peated cycles of conformational dis tortion and energy minimization where the distortions focus on normal mode guided changes in a user selected set of key torsion an gles These key torsional bonds must be selected by clicking the corresponding bonds in the chemi cal structure of the system shown in the graphical Tork conforma tion search window the right hand pane of the M2 GUI Each se Parameters for Tork iC ES Number of probes fi Energy cutoff 20 0 Sampling type fi Minimization type fi Distorsion energy bon threshold 500 0 Number of energy B thresholds 3 Number of steps fi 00 Step size o Random seed 3971 Torsion diff for 10 0 overlap checking IV Use GB as the implicit solvent model Figure 5 6 Dialog box to set Tork conforma tional search parameters 5 3 TORK CONFORMATIONAL SEARCH 23 lected bond will be highlighted and will also be listed in the Select ro tatable bonds box in the left hand pane The Tork Parameters button brings up the Parameters for Tork window Figure 5 6 which provides access to the main parameters of the Tork conforma tional search
43. s M2_1win exe Main executable to run energy minimization and Tork con formational search 10 CHAPTER 3 INSTALLATION M2_2win exe Main executable to run HA MS free energy calculation m2uhbd win exe Executable to run Poisson Boltzmann calculation m2uhbd is a version of the program UHBD 20 with our minor modifications for compatibility with M2 The m2uhbd software is available for free non commercial use from the University of Houston To obtain it please email Dr James Briggs jbriggs uh edu stating your interest in obtaining the m2uhbd software Vcharge exe The executable to calculate Vcharge conformation independent charges This can be obtained without charge for noncommercial use from www verachem com and the license file vcharge 1lic should be obtained accordingly Create a repository directory folder to contain all of the files associated with Mining Minima version 2 4 2 An example is c Program Files M2_2 A 2 Do not use a directory whose pathname includes spaces for example do not use a subfolder of the Windows Documents and Settings folder At this point the installation of Mining Minima version 2 A 2 is complete and you can now try running Mining Minima version 2 A 2 by double clicking the M2 py icon found in your Mining Minima repository directory This should activate the M2 GUI Chapter 4 Tutorial A Sample M2 Calculation This section details the steps to be followed in order t
44. s into the site packages repository located in the newly built Python 2 2 2 path for example c Python22 Lib site packages 6 Using an appropriate extraction utility open the OpenGL_2 0 1 03_install rar file Extract the files into the site packages repository located in the Python 2 2 2 path see Step 8 Now rename the directory called c Python22 Lib site packages OpenGL_2 0 1 03_install to c Python22 Lib site packages OpenGL 7 Copy the file glut32 d11 to the c WINDOWS SYSTEM32 directory 8 Copy the file PmwB1t py to the c Python22 Lib site packages Pmw Pmw 1_1 lib directory You must overwrite the copy currently in that directory CHAPTER 3 INSTALLATION 9 Double click on the b1t2 4u for 8 3 exe icon to install the BLT packages The installation directory does not matter the default directory c Program Files tcl is acceptable After installing the BLT packages locate the bin sub directory of the BLT installation directory Copy the file BLT24 d11 from the bin directory into the directory c Python22 DLLs 10 Copy the file psftp exe into the c Python22 directory 11 Copy the file plink exe into the c Python22 directory 12 Finally the newly created Python22 directory must be added to the PATH environment variable To accomplish this Click START SETTINGS CONTROL PANEL Double Click SYSTEM Select the ADVANCED tab Select the ENVIRONMENT VARIABLES button Highlight the PATH variable from the list of SY
45. tandard deviations of the Gaussian along the mode or that distance which causes any torsion angle to change by more than 60 6 A number of modes defined by the user See Section 5 5 with the lowest force constants are also scanned to check and correct for anharmonicity as follows For each scanned mode the scan starts at the local energy minimum and distorts the molecule along the Bond Angle Torsion eigenvector in small steps until the integration limits described above are reached At each step the energy and Boltzmann factor are calculated This scan is done in the positive and negative direction along the mode The trapezoid rule is then used to estimate the integral of the Boltzmann factor along the mode and this scanned integral is compared with the harmonic one already obtained above If the absolute value of the difference is greater than a cutoff value of 0 5 kcal mol then the scanned value is used in place of the harmonic value The free of the energy well 7 is thus estimated as a sum of con tributions from each mode where most modes end up being treated harmonically while a few that prove to be anharmonic based on their mode scans are treated by the scanning method Note that this empirical approach does not account for any anharmonicity that may be associated with distortions along combinations of modes The energy E r can be decomposed into the sum of the potential energy U r and the solvation energy W r both f
46. ter an additional contribution of 7 03 kcal mol must finally be added to the differ ence in chemical potential according to Equation 2 2 The configurational entropy change AB rig is then calculated using Equation 2 7 thus this en tropy change includes the 7 03 kcal mol standard state adjustment 21 In the present example the computed binding free energy should be close to 22 kcal mol Chapter 5 User Interface Components M2 Steps Free Energy Calculation gt CB amp B5 Steps Tools 615 033 kcal mol FE Parameters Load Run Stop Display Atom Name sl For Selected Atoms zl In Displayed Structure Sl Conformation viewer Lab Color by Element el Center Energy minimization Figure 5 1 Main M2 window with cucurbituril guest complex Figure 5 1 shows the first window that is displayed upon executing the M2 program The interface has two menu options Steps and Tools The Steps option provides the user with the standard series of computational tasks used to complete an M2 calculation e Minimization Starting conformation is subjected to an initial energy mini 17 18 CHAPTER 5 USER INTERFACE COMPONENTS M2 STEPS mization e Tork Tork algorithm is used to discover new low energy conformations e Filtering Duplicate conformations are eliminated e Free Energy Free energies of conformations are calculated e Free Energy Correction Free energies are corrected with a more detailed sol
47. tton bring up the Minimization Parameters window Figure 5 3 which allows changes to the default procedural and energy parameters which are de fined as e TN Minimization Steps Maximum number of TN iterations to carry out e TN Tolerance Termination criterion based on root mean square RMS gra dient of the energy e TN Frequency of Output Number of TN steps between updates to the out file The parameters set by default here are considered reasonable choices but they may be changed One can select the potential energy terms bond angle dihedral improper Coulombic and vdW to be included The Generalized Born GB sol vation model is selected by default and if it is used its parameters can be adjusted by clicking on the GB Parameters button and using the GB Parameters window Figure 5 4 The GB options are as follows e Fixed Dielectric Constant For Solute The interior dielectric constant of the molecule default 1 e Fixed Dielectric Constant For Solvent The solvent dielectric constant default 80 for water at 298K e Use ideal geometry in radii calculations Refers to an older implementation of GB in which the bond lengths used in calculating the GB cavity radii were always kept at their ideal values based on the force field e Output details of GB calculations Provides greater detail regarding GB cal culations in the output screen e Atom radii are averaged with probe radius A method of setting initial atomi
48. unctions of the conformation r 7 8 M2 approximates the potential energy with an empirical force field which in the present implementation must follow the same widely used functional form found in current versions of for example CHARMM 9 10 11 12 and AMBER 13 14 During conformational search and HA MS calculations a generalized Born model 15 16 is used for the solvation energy Solvation energies are subsequently cor rected toward the Poisson Boltzmann Surface Area model 17 18 based upon one finite difference solution of the linearized Poisson Boltzmann equation and one surface area calculation for each energy minimum i as previously described 19 m2uhbd win exe or m2uhbd exe obtainable from Prof James Briggs U of Hous ton The M2 calculations also yield an estimate of the change in the Boltzmann averaged sum of the potential and the solvation energies on binding A U W 4 CHAPTER 2 OVERVIEW For this purpose each energy is considered to be purely harmonic in form so that equipartition applies Thus if the energy at the base of energy well 7 is U W then the mean energy in the well is approximated as AN 6 2 4 U W U Wi S RT where the third term is the equipartition contribution Eeg The mean across all M energy wells then is M 2 5 U W Li alU W AN 6 py D 2 Applying this expression to the host the guest and their complex yields that SY AU ew Da where
49. xport TRJ Writes out a trj file for the molecular conformations currently displayed in the M2 graphics window e Clear window Unload all molecules for a new calculation Chapter 7 M2 Files Contents and Format 1 psf Protein structure file a basic data file format used by the program CHARMM 2 top M2 molecular topology file with the following contents ATOM BLOCK Atom index CHARMM atom type mass charge au Lennard Jones parameters kcal mol and A and alternate Lennard Jones parameters for 1 4 interactions BOND BLOCK Indices of the bonded atoms force constant kcal mol A and equilibrium bond length A ANGLE BLOCK Indices of the atoms forming each angle force constant kcal mol radian and equilibrium value of the harmonic angle term PROPER DIHEDRALS Indices of the atoms forming the dihedral angle the coefficient of the sinusoidal torsional energy term kcal mol the multiplicity of the torsion and phase of the torsion radians IMPROPER DIHEDRALS Indices of the atoms forming the dihedral an gle the harmonic force constant kcal mol radian and the equilibrium value of the angle NBFIX BLOCK Special Lennard Jones parameters kcal mol A which override the standard combination rules for the specified atom type pairs NFINAL numbers of atoms bonds angles proper dihedrals and im proper dihedrals The final integer can be ignored 3 crd CHARMM coordinate file 4 trj M2 trajectory
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