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QSite User Manual - The Friesner Group

1. 37 solvation method and electrostatic treatment 28 GOTT EE rennes es s asares 30 explicit Waters sind thin 30 spin density gurface 39 spin multiplicity sssissssessssosssssctss nnsnnnsnsesenrn 23 spin unrestricted open shell calculations 23 step size MM energy minimization 35 23 steric clashes in energy minimization 35 structures IMPOT NS s smsmssssssrsresrersrsrrsrsrrnrrrsrsn rar 4 Surface DOX Size 40 surface grid density 41 SUT ACES ADs sccscatessesivessssetsosssisdesazadscantveseavesdoses 40 T transition metals possible problems with 31 44 transition state optimization methods 38 W waters SXPlICit set nie mn eines 30 QSite 5 0 User Manual 69 70 QSite 5 0 User Manual 120 West 45th Street 101 SW Main Street 3655 Nobel Drive Dynamostra e 13 QuatroHouse Frimley Road 29th Floor Suite 1300 Suite 430 68165 Mannheim Camberley GU16 7ER New York NY 10036 Portland OR 97204 San Diego CA 92122 Germany United Kingdom SCHR DINGER
2. Start Read Write Close Help Figure 4 3 The Potential tab of the QSite panel The variables in the above formulae are defined as follows e E 1s the electrostatic interaction in kcal mol e q and d are the partial atomic charges on atom i and j e ris the distance in A between atoms i and j e Eis the Dielectric constant see below Dielectric constant This text box specifies the value of the dielectric constant used in the electrostatic calcula tions In molecular mechanics calculations it is often impractical to include the nonbonded electro static and van der Waals interactions between every pair of atoms For large systems many such pairs are separated by a great distance and contribute little to the interaction energy Judi cious truncation of the non bonded interactions between widely separated pairs of atoms is an important strategy for reducing the resources needed for calculations on large systems QSite 5 0 User Manual 29 Chapter 4 Running QSite From Maestro 30 At present only residue based cutoffs are supported for calculations set up in Maestro This means that all atoms within complete residues that have any pair of atoms within the cutoff distance will be included in the non bonded interaction list The list is updated periodically as the geometry changes because residues may move inside or beyond the cutoff radius Use non bonded cutoffs Select this option to truncate nonbo
3. Type SSCHRODINGER qsite for a usage summary of the gsite command or see Chapter 5 for information on running QSite from the command line 4 2 The QM Settings Tab The QM Settings tab is used to enter information for the QM job and to define the QM region QM job information includes the quantum mechanical method to be used the charge and spin multiplicity of the QM system and other keywords and options that may be required by Jaguar The QM region can be defined by one of the following methods e Selecting the ligand metal ions or other disconnected species not covalently bonded to the protein e Specifying cuts between certain covalently bonded atoms in connected peptide residues QSite cuts are specially parameterized frozen orbital boundaries between the QM and MM regions They can be placed between an alpha carbon and a side chain side chain cuts or between an alpha carbon and the backbone to one side backbone cuts which must be made in pairs to add the residues between them to the QM region In QSite 5 0 QSite cuts are parametrized to the OPLS_2001 force field However you can use either the OPLS_2001 or the OPLS_2005 force field for calculations QSite 5 0 User Manual 21 Chapter 4 Running QSite From Maestro Cuts in a protein ligand complex must be between atoms in peptide residues Covalently bound ligands can be included in the QM region but only along with attached protein atoms The QM region mu
4. Chapter 3 Protein Preparation 16 3 2 2 Checking for Steric Clashes You should make sure that the prepared site accommodates the co crystallized ligand in the restraint optimized geometry obtained from the structure preparation Steric clashes can be detected by displaying the ligand and protein in Maestro and using the Contacts folder in the Measurements panel to visualize bad or ugly contacts Maestro defines bad contacts purely on the basis of the ratio of the interatomic distance to the sum of the van der Waals radii it assigns As a result normal hydrogen bonds are classified as bad or ugly contacts By default Maestro filters out contacts that are identified as hydrogen bonds and displays only the genuine bad or ugly contacts If steric clashes are found repeat the restrained optimization portion of the protein preparation procedure but allow a greater rms deviation from the starting heavy atom coordinates than the default of 0 3 A Alternatively you can apply an additional series of restrained optimizations to the prepared ligand protein complex to allow the site to relax from its current geometry 3 2 3 Resolving H Bonding Conflicts You should look for inconsistencies in hydrogen bonding to see whether a misprotonation of the ligand or the protein might have left two acceptor atoms close to one another without an intervening hydrogen bond One or more residues may need to be modified to resolve such an acceptor acceptor
5. Given the number of atoms in the typical receptor ligand complex it can be hard to identify the ligand In this exercise you will locate the ligand and set up the display to view only the ligand and the protein residues close to it 1 From the Undisplay toolbar button menu choose Protein a The protein is undisplayed and only the ligand remains visible QSite 5 0 User Manual Chapter 2 QSite Tutorial 2 From the Display residues within N of currently displayed residues toolbar button menu choose 3 D r L Ben The residues around the ligand are now displayed 3 Click the Fit to screen toolbar button The view zooms in so that the structure fills most of the Workspace 4 From the Draw bonds in tube toolbar button choose Molecule Q 5 Click on an atom in the ligand molecule such as the phosphorus colored purple The ligand is now displayed in the tube representation and is clearly distinguished from the protein residues 2 5 Selecting the QSite Job Type Follow the instructions below to open the QSite panel and set the job type 1 In the main window choose QSite from the Applications menu The QSite panel is displayed 2 In the Potential tab ensure that OPLS 2005 is selected in the Force field option menu and deselect Use non bonded cutoffs this stabilizes the minimization for this small receptor 3 In the QM Optimization tab ensure that Minimization is selected in the Method option me
6. File name Description Jobname mae Jobname 1og Jobname in Jobname out Like Jaguar QSite Maestro format structure file The output Maestro file contains an index number like the restart file jobname nn mae However if jobname already contains an index number it is incremented in the output Maestro file name QSite log file The Log file captures standard error messages in text form Includes both Jaguar and Impact log information The input file for a QSite calculation Includes both Jaguar and Impact input At various points in the job an input file restart file containing the latest geometry and settings is written This file is named jobname nn in where nn is a two digit number starting with 01 This number is incremented if jobname already contains an index number QSite output file Includes both Jaguar and Impact output writes a restart file at various stages of the calculation The restart input file has an index number inserted into the file name for the first restart it is jobname 01 in The output Maestro structure file also includes the index number its name is jobname 01 mae Running QSite with this first restart file produces a restart file named jobname 02 in and a Maestro file named jobname 02 mae 5 2 The qsite Command The gsite command provides both the means to submit QSite jobs and to interact with the Job Control facility to query and control the progress of a job To
7. 4 10 Running QSite Jobs When you have set the options in the QSite panel tabs to the desired value click the Start button to open the Start dialog box In this dialog box you can set up the job options then submit the job to a host for execution For details of the features of this dialog box see Section 4 2 of the Job Control Guide When choosing job and host options you should take note of the following points e QSite does not automatically assign new names to jobs or files If files of the same name exist a warning is displayed before any files are overwritten e You can use multiple CPUs for parallel processing of the QM part of the calculation if the host has multiple processors e Do not use parallel processing for jobs that include continuum solvation treatment as they will fail if you do When you have selected job options click the Start button to run the job QSite jobs can be monitored in the job Monitor panel If a QSite job needs to be restarted it can be restarted from Maestro or from the command line To restart a job from the command line simply run QSite with the restart file specified as the input SCHRODINGER qsite job options jobname 01 The restart input file has an index number inserted into the file name for the first restart it is Jobname 01 in Running with this file produces a restart file named jobname 02 in and so on Likewise the output structure file has an index number inserted into the f
8. B Philipp D M Friesner R A Chem Phys Lett 2000 321 113 Murphy R B Philipp D M Friesner R A J Comput Chem 2000 21 1442 QSite 5 0 User Manual Chapter 6 QSite Technical Notes Dunietz B D Beachy M D Cao Y Whittington D A Lippard S J Friesner R A Large scale ab initio quantum chemical calculations of intermediates in the soluble methane monooxygenase catalytic cycle J Am Chem Soc 2000 122 2828 2839 Lippard S J Berg J M Principles of Bioinorganic Chemistry University Science Books 1994 Porter T D Coon M J Cytochrome P450 multiplicity of isoforms substrates and catalytic and regulatory mechanisms J Biol Chem 1991 266 13469 13477 QSite 5 0 User Manual 63 64 QSite 5 0 User Manual Getting Help Schr dinger software is distributed with documentation in PDF format If the documentation is not installed in SCHRODINGER docs on a computer that you have access to you should install it or ask your system administrator to install it For help installing and setting up licenses for Schr dinger software and installing documenta tion see the Installation Guide For information on running jobs see the Job Control Guide Maestro has automatic context sensitive help Auto Help and Balloon Help or tooltips and an online help system To get help follow the steps below e Check the Auto Help text box which is located at the foot of the main window
9. column and the basis set used is given in the Basis column You can select multiple rows and apply a basis set to the selection Pick option and menu Select this option to pick atoms for which you want to change the basis set Three of the options on the menu are the same as in the QM Region tab and work in the same way The Hydrogen cap option is not present instead there is an Atom option that enables you to pick individual atoms The atoms you pick are marked with green axes if Show markers is selected and they are also selected in the basis set table QSite 5 0 User Manual 27 Chapter 4 Running QSite From Maestro 28 Show markers option When this option is selected the atoms that are selected in the table or picked are marked with green axes Basis set option menu Choose the basis set for the selected rows in the basis set table from this option menu By default the basis set used for the entire QM region is LACVP which uses 6 31G for non transition metals This is the basis set used in the parameterization of the frozen orbital cuts Note The inclusion of frozen orbital cuts enforces the use of 5D for the d functions 4 3 The Potential Tab The Potential tab provides options for the definition of the potential energy functions used in the molecular mechanics part of the calculation One of these continuum solvation affects the QM potential energy as well Force Field The two available force fields are
10. 7 The MM Minimization tab of the QSite panel Convergence criterion Choose the quantities used for the convergence criteria from this option menu Either or both of two criteria energy change and gradient can be specified The options control the avail ability of the Energy change criterion and Gradient criterion text boxes Energy change criterion Specify the value of the energy change criterion in this text box The default value is 107 kcal mol but any positive value is allowed The criterion is satisfied if two successive energies differ by less than the specified value Gradient criterion Specify the value of the gradient criterion in this text box The default value is 0 01 kcal mol A but any positive value is allowed The criterion is satisfied if the norms of two succes sive gradients differ by less than the specified value QSite 5 0 User Manual Chapter 4 Running QSite From Maestro Update long range forces every n steps Specify the frequency with which long range forces are updated for Truncated Newton minimi zations in this text box Between these intervals estimates of these forces are used Every 10 steps is the default smaller numbers more frequent updates can be used to improve conver gence but will make the optimization slower Larger numbers for n may speed the calculation but the maximum recommended value is 20 Long range force cutoff gt d Angstroms Specify the distance beyond whi
11. Chapter 4 Running QSite From Maestro 20 e QM Settings specify the QM region and other QM options e Potential choose settings for the MM potential energy function e MM Constraints set up atom constraints for atoms in the MM region e QM Constraints set up constraints for atoms in the QM region e MM Minimization set up energy minimization of the MM region e QM Optimization select and set up the job task These tabs are described in later sections of this chapter Below the tabs are several action buttons which are described in a subsection below 4 1 1 Source of Structure Input Input for QSite single point jobs minimization jobs and standard transition state searches must be a single Project Table entry To use a system consisting of two or more entries as the input choose Merge from the Entry menu in the Project Table panel create a combined entry and run the simulation on that entry LST and QST transition state searches are a special case here the input is specified in the QM Optimization tab You can select the source of input from the Use structures from option menu The options are described below Workspace included entry This is the default option The structure that is currently included in the Workspace is used as input to the job This includes whatever atoms molecules or entries are part of the structure even atoms that have been undisplayed You must choose this option if you want to use
12. MM minimization in which the QM region is frozen The final geometry has an RMS deviation of 0 6 A with respect to the non hydrogen atoms of the crystal structure a reasonable level of accuracy In a general study of a sys tem like this the initial cost of this minimization would be amortized over similar runs in which the QM region would be perturbed by changing the ligand for example since these subsequent runs would have a good initial geometry As an initial calibration of the energetics we optimized the doublet and quartet spin states of the system The doublet was found to be 14 kcal mol lower in energy This is in accord with qualitative EPR data 8 that indicates that Fe is in a low spin state when a six fold Fe coordination site involves dative bonding to the ligand The substrate free system with the camphor above the heme ring was found after full QM MM optimization to have a high spin quartet ground state with the doublet 15 kcal mol higher in energy This ordering of spin states is also in agreement the experimental ordering 9 6 6 References 1 Bofill J M J Comp Chem 1994 15 1 Murtagh B A Sargent R W H Comput J 1970 13 185 Powell M J D Math Prog 1971 I 26 Peng C Schlegel H B Isr J Chem 1993 33 449 Gogonea V Su rez D van der Vaart A Merz K M Jr Curr Opin Struct Biol 2001 11 217 223 Philipp D M Friesner R A J Comput Chem 1999 20 1468 Murphy R
13. QSite 5 0 User Manual v vi QSite 5 0 User Manual Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SSCHRODINGER maestro File names directory names commands envi ronment variables and screen output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys uppercase Links to other locations in the current document or to other PDF documents are colored like this Document Conventions In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets 1 enclose optional items and the bar symbol separates items in a list from which one item must be chosen Lines of command syntax that wrap should be interpreted as a single command File name path and environment variable syntax is generally given with the UNIX conven tions To obtain the Windows conventions replace the forward slash with the backslash in path or directory names and replace the at the beginning of an environment variable with a at each end For example SCHRODINGER maestro becomes 3SCHRODINGER maestro In this document to type text means to type the required text in the specifi
14. QSite From Maestro 4 2 1 General Settings Method The options for the QM method include several density functional theory methods DFT B3LYP DFT PWB6K DFT MO6 DFT MO6 2X DFT MO6 L DFT MO6 HF DFT MO5 DFT MO5 2X Hartree Fock Hartree Fock and local Mgller Plessett perturbation theory Local MP2 The DFT User defined option is selected when an input file is read that specifies a functional other than those available from this menu Otherwise this option is not available For more information on the functionals see Section 3 3 of the Jaguar User Manual Spin unrestricted option Select this option to perform a spin unrestricted open shell calculation This option is only available with the Hartree Fock and DFT B3LYP methods Otherwise open shell calculations will be performed with the restricted open shell methods Charge This is the net charge of the QM region of the system Maestro updates the charge to a reason able value whenever a new residue or ion is added to the QM region If a discrepancy appears edit the value If this value does not match the sum of the formal charges of the atoms in the QM region Maestro displays a warning message but allows you to proceed Multiplicity Check that this is the associated spin multiplicity of the QM region of the system 1 for singlet 2 for doublet etc Edit the value if necessary If there is a discrepancy between the total charge and the multiplicity the Jaguar calculatio
15. be added for QSite calculations 5 3 2 The qmregion Section The qmregion section contains specifications that define the QM region in terms of frozen orbital cuts free ligands ions or cofactors and hydrogen caps The specifications are made in a free format table using the keywords given in Table 5 5 The first five keywords can be combined in any fashion provided they define a valid cut or free molecule The hydrogen cap keywords hcapqm and hcapmm must be used together A sample qmregion section is given below This is a rather artificial example that contains all possible types of specification of the QM MM boundary QSite 5 0 User Manual Chapter 5 Running QSite from the Command Line Table 5 5 Keywords used in the qmregion section Keyword Description molid Molecule number chain Chain name This keyword is optional and can be used to distinguish chains if more than one is present resnum Residue number and insertion code qmatom QM atom for a cut Can be specified with the PDB atom name or the atom number optionally prefixed by the atom name and an underscore mmatom MM atom for a cut Can be specified with the PDB atom name or the atom num ber optionally prefixed by the atom name and an underscore If omitted all atoms in the molecule are taken to be in the QM region hcapqm QM atom for cuts made by the hydrogen cap link atom method The atom can be specified by the Maestro atom number optionally prefixe
16. between the reactant and product structures for only the atoms seen by the QM program Jaguar these atoms include those in the QM region plus a small number of MM atoms located at the QM MM interface This proce dure includes a least squares fit of the interfacial MM atoms in the interpolated geometry to the respective atoms in each of the reactant and product geometries The interpolated TS QM region plus interfacial MM atoms are then inserted into the pure MM structure of the best fitting case reactant or product using the transformation found from the least squares fitting The LST QST guided search for cases 2 or 3 then proceeds as it does for Jaguar by first restricting the optimizer to search along the circular curve connecting the reactant TS and product structures Again only the QM plus interfacial MM atoms seen explicitly by Jaguar are used The pure MM atoms are adiabatically minimized at each step Once the optimizer approaches or finds a maximum energy TS structure along this reactant product curve the TS search proceeds along the Hessian eigenvector that is most similar to the tangent to the circular curve This process continues until a saddle point with one negative eigenvalue corre sponding to an imaginary frequency is found QSite 5 0 User Manual Chapter 6 QSite Technical Notes In contrast a simple transition state search case 1 just involves the attempt by the optimizer to maximize the energy along the lowe
17. constraints see the Constraints tab Section 4 4 on page 31 because the constraints are applied to the Workspace structure Project Table selected entry Select this option to use the entry that is currently selected in the Project Table This may be different from the structure in the Workspace Because atom constraints are applied to the Workspace structure they are ignored if this option is chosen 4 1 2 Action Buttons The lower part of the QSite panels contains a row of action buttons Apart from the standard Close and Help buttons for closing the panel and opening the help viewer there are three buttons for job related actions described below QSite 5 0 User Manual Chapter 4 Running QSite From Maestro Start Click the Start button to open the Start dialog box Section 4 10 describes how to start jobs using the Start dialog box Read The Read button reads a QSite input file and imports the associated structure It opens a file selector in which you can navigate to the desired input file Write The Write button writes out all the files required for the job but does not run the job Once the files required for the job are written by Maestro the job can be run from the command line in a terminal window using the syntax SCHRODINGER gsite job options jobname where jobname in is the input file for the job in question and job options is a list of options for the job The log output is written to jobname 10g
18. hydrogen bond dimerization energies and to reproduce LMP2 cc pVTZ f relative conformational ener gies for the alanine dipeptide more accurately than does a molecular force field such as OPLS AA see Ref 6 Table 6 2 RMS deviations kcal mole of rotamer side chain conformational energies for HF 6 31G QM MM B3LYP 6 31G QM MM and OPLS AA relative to cc pVTZ f LMP2 QM MM QM MM Residue QM HF QM DFT OPLS AA Phe 0 18 0 14 0 18 His 1 14 1 10 1 05 Asn 0 38 1 36 2 29 Val 0 21 0 41 0 62 Trp 0 71 0 25 0 75 Tyr 0 37 0 29 0 40 Leu 0 77 0 90 0 40 Met 1 10 1 21 1 82 Gin 1 48 1 03 2 70 Glu 2 61 2 69 3 34 Cys 0 61 0 62 3 52 Lys 1 44 1 29 4 22 Ile 1 03 0 56 1 19 Asp 1 11 1 91 2 51 Arg 1 67 3 50 2 90 QSite 5 0 User Manual Chapter 6 QSite Technical Notes 6 5 An Illustrative Application Cytochrome P 450 is an enzyme whose variants are ubiquitously distributed across a wide variety of organisms A human version of the enzyme in the liver is of great importance phar maceutically because it is involved in a significant fraction of toxicity and drug metabolic path ways While a high resolution structure of a form of the human enzyme relevant to questions of toxicology and metabolism does not yet exist such structures are likely to be produced in the next few years either experimentally or via homology modeling This will open the possi bility of computer modeling of these critical processes It is very difficult to study t
19. is as follows SCHRODINGER gsite command command options The available commands are listed in Table 5 3 Table 5 3 Syntax for qsite commands Command Description jobs name status kill name status stop name status purge name help machid platform sysreq Show status of the specified QSite jobs or list the jobs that have the spec ified status Kill the QSite jobs with the specified job name or job status Stop the QSite jobs with the specified job name or job status at the end of the current calculation stage Remove records for the specified jobs from the job database If no name is given all completed jobs are purged Display usage message Report the hardware and software configuration This command gives the same output as the SCHRODINGER machid command Report information on the hardware platform This command gives the same output as the SCHRODINGER plat form command Report any system requirements for QSite and whether they are met 5 3 The QSite Input File The input file for QSite combines the input required for Jaguar and the input required for Impact The file is in the same format as the Jaguar input file and the input sections that relate to the QM part of the calculation are the same as in the Jaguar input file For details on these sections see Chapter 8 of the Jaguar User Manual There are no zmat zmat2 or zmat3 sections are in the input file because all
20. of range for all but the most powerful supercomputers e QSite can run the rate limiting QM part of the code on parallel processors so that reason able throughput can be achieved for the relatively large 100 200 atom QM regions that can be necessary to reliably model active site reactive chemistry e QSite incorporates a Poisson Boltzmann continuum dielectric treatment of aqueous sol vation This treatment is capable of handling the QM and MM regions simultaneously and includes an analytic gradient so that geometry optimization in solution can be per formed Inclusion of solvation will be critical in some but not all applications an obvi ous case being calculation of pK values of ionizable protein side chains or of ligand groups that interact with the protein Maestro makes it easy to set up a QSite calculation For example its QSite interface can be used to readily identify the QM residues of the protein via mouse clicks and to specify whether the QM MM cut is to be placed in the backbone or side chain The 6 31G basis set is used in the interface region but other basis sets can be used elsewhere For example the geometry can be optimized with the 6 31G basis set and a large high quality basis set can then be used in a reactive region to determine accurate single point energies We have used this strategy very successfully in our QM based modeling of the protein methane monooxygenase 7 and expect it to work for a wide range
21. or donor donor clash Some of these clashes are recognized by the preparation process but cannot be resolved by it The preparation process may have no control over other clashes An example of the latter typi cally occurs in an aspartyl protease such as HIV where both active site aspartates are close to one or more atoms of a properly docked ligand Because these contact distances fall within any reasonable cavity radius the carboxylates are not subject to being neutralized and will both be represented as negatively charged by the preparation process However when the ligand inter acts with the aspartates via a hydroxyl group or similar neutral functionality one of the aspar tates is typically modeled as neutral If residues need to be modified follow these steps 1 Place the refined protein ligand complex in the Workspace 2 Examine the interaction between the ligand and the protein and or the cofactor 3 Use your judgment and chemical intuition to determine which protonation state and tau tomeric form the residues in question should have 4 Use the structure editing capabilities in Maestro to resolve the conflict see Section 3 8 of the Protein Preparation Guide for procedures QSite 5 0 User Manual Chapter 3 Protein Preparation 5 Re minimize the structure It is usually sufficient to add the proton and perform about 50 steps of steepest descent minimi zation to correct the nearby bond lengths and angles Because t
22. orbital cuts or hydrogen caps the resulting structure and properties will generally be erroneous The handling of frozen orbitals involves a parameterization for the potential about the frozen bond which relies on particular values for the partial charges of the atoms near the QM MM interface In general the charges in the Maestro structure file will not be appropriate for use with frozen orbitals ESP charges written to the output Maestro file from jobs with frozen orbitals or hydrogen caps are only for the QM atoms and will not usually add up to the appropriate molec ular charge Skip force field checks By default Impact performs a number of tests during atom typing to guide selection of optimal force field parameters for the atoms in the input structure The tests are applied to both the MM and the QM regions For transition metals force field parameters are more limited than for the common p block elements so when the structure contains transition metals these atom typing tests can fail and cause the job to halt The force field is not used if the metals are in the QM region By selecting this option the force field checks are bypassed and the metal atoms do not cause the job to fail 4 4 The MM Constraints Tab The MM Constraints tab is used to apply constraints to the Cartesian coordinates of selected atoms in the MM region Specified atoms can be frozen at their input coordinates frozen atom constraints or they can be constrained
23. rotated as the molecular geometry changes and its interaction with both the QM and MM regions must be properly represented The charge distribution must be empirically corrected to reproduce the fully quantum chemical result QSite does this by placing a charge in the middle of the frozen bond QSite not only includes appropriate energy expressions for this representation but also the analytical gradients that are critical to applications that involve geometry optimization e The QM and MM regions interact via two mechanisms Coulomb interaction between MM charges and the QM wavefunction and van der Waals interaction between QM and MM atoms both of which employ van der Waals parameters e Specialized correction terms are used for stretches bends and torsions involving the atoms directly associated with the frozen orbital interface These terms are fit to repro duce quantum chemical conformational energies of the template molecules Again QSite has gradients for all of these terms as well as energy expressions The torsional correction parameters were determined from a library of high quality QM calcu lations on rotamer states for dipeptides Beginning with roughly 300 geometries obtained via QSite 5 0 User Manual 57 Chapter 6 QSite Technical Notes 58 conformational search using OPLS AA the structures were optimized at the HF 6 31G level and single point LMP2 cc pVTZ f relative energies were computed Finally one dime
24. the MM and the QM solvation functions is the Poisson Boltzmann Solver PBF selecting Use continuum solvation automatically sets both solvation functions to PBF in the Jaguar input file isolv 2 The Surface Generalized Born SGB and Analytic Generalized Born AGB methods are not available for QSite calculations The Continuum Solvation panel options available for PBF are as follows PBF resolution The Poisson Boltzmann solver involves a finite element calculation on a grid The grid spacing controls the accuracy of the PBF calculation and the time required The default Low resolution suffices for most protein work If needed greater accuracy can be achieved by choosing Medium or High resolution QSite 5 0 User Manual Chapter 4 Running QSite From Maestro e PBF displacement threshold This text box specifies how far in A any atom may move from the coordinates used in the previous PBF calculation before a new PBF calculation must be performed If no atom has moved this distance the previously calculated PBF energy and forces are used Use atomic partial charges in structure file With this option you can choose to use the atomic partial charges that are stored in the input structure file rather than the partial charges that are assigned by the force field This option should only be used when the QM region consists of one or more non covalently bound molecules If you use this option for a system in which you make frozen
25. the MM region e None Ignore electrostatic interactions between the QM and MM regions entirely Van der Waals interactions are still included Use wave function in input file Use Hessian in input file These options allow you to read the wave function and the Hessian from the input file and make use of them in the calculation This capability is particularly useful when restarting a calculation 4 2 2 QM Region Subtab In this subtab you set up the QM region The total number of atoms in the QM region is displayed below this subtab To define the region choose a type of cut from the Pick option menu and pick atoms to define the cut If you want to delete a cut select it in the table and click Delete To start over with the selection of cuts click Delete All QM region table The cuts that define the QM region are listed in the table The Type column gives the cut type and corresponds to the choice made from the Pick option menu to define the cut The Name column identifies the cut e Side chain Residue name and number Entire residue Residue name and number Free ligand ion Molecule number e Hydrogen cap QM atom number MM atom number When you have finished picking to define a cut or a set of QM atoms table rows are added for each cut or atom set To delete a cut select the cut in the table and click Delete QSite 5 0 User Manual Chapter 4 Running QSite From Maestro Pick option and menu Select th
26. 1 Potential ob 6 29 product installation 65 protein adjustment of structure eneneneseneenennen 14 misprotonation Of 16 protein preparation Overview 13 Q QM Constraints tab QM methods QM Optimization tab 38 OM options sists isccsed taecesgcectserietseavesssectecsesestests 23 QM region adding entire residues to 25 boundaries soniers innean 21 defining seersieiasesreiceesinrisisiseniaisisi seers 6 24 interaction with MM region 57 pet charges renden 23 QM Settings tab 7 22 2 QM MM interface rent 57 QM MM defined ssssssessseesssessessesersersesrsrsesses 1 QSite calculations TESUICH NS 275ssesderesnssessnsnnsersesnsnasnsskssksreresnsrs 19 unavailable solvation methods 30 QSite brief description 1 Quadratic Synchronous Transit QST method 39 quasi Newton method 38 R residues adding to the QM region 25 restarting e DEE 43 restrictions backbone cuts s ssssessrsrsorsrerssrsrsrenrrrsrerrnrr nn en 25 ntry selectionner 19 OESTE a A E E E EE 21 parallel processing e e eseseeeseereeerereeeeeee 30 solvation method 30 rigid and relaxed scans 41 S scan coordinate adding essen 41 PANGS sci asssvscaecatunsustgeasson saranda reeacevtiveues veadesed 42 Index SCAN EE 42 Schr dinger contact information 66 side chains adding to the QM region 25 single point energy calculations
27. 5 and the ligand s hydrox amate group Figure 2 5 You might have to rotate the structures to locate a good view of the hydrogen bonds as shown in the figures QSite 5 0 User Manual 11 12 QSite 5 0 User Manual Chapter 3 Protein Preparation The quality of QSite results depends on reasonable starting structures Schr dinger offers a comprehensive protein preparation facility in the Protein Preparation Wizard which is designed to ensure chemical correctness and to optimize protein and protein ligand complex structures for use as input For QSite the entire system both MM and QM regions must be prepared so as to satisfy the requirements of Impact OPLS_2001 while the QM region must satisfy the requirements of Jaguar It is strongly recommended that protein structures imported from non Maestro sources such as PDB structures be treated with the protein preparation facility in order to achieve best results For the molecular mechanics simulations using Impact with OPLS force fields structures must be all atom explicit hydrogens and there must be no covalent bonds between ligand atoms and protein atoms including protein metal atoms Bond orders and formal charges must be correct For Jaguar calculations on the QM region structures must be three dimensional and correct have reasonable starting bond orders and formal charges 3 1 Protein Preparation Procedure A typical PDB structure file consists only of heavy atoms can con
28. Checking the Protein Structures 15 3 2 1 Checking the Orientation of Water Molecules AA 15 3 2 2 Checking for Stere Clashes 4 E nase 16 9 2 3 Resolving H Bonding Conflieis 4 ana 16 Chapter 4 Running QSite From Maestro 19 4 1 The QSite Panel EE 19 41 1 Source of Structure Inputs sei ale 20 A2 Aon TE 20 QSite 5 0 User Manual Contents 4 2 The QM Settings E EE 4 2 1 General Settings s seine sente ennemie ain ia 4 2 2 OM Region Subtab EE 4 2 3 OM Basis EE 4 3 The Potential Tab iisacisnnndnn eege Ha nl 4 4 The MM Constraints Tab 4 5 Th QM Constraints Tab 4 6 The MM Minimization Tab 4 7 The QM Optimization Tab 4 7 1 SalCUl e ee WEIER 4 8 RN El Ce CT EE 4 97 bereede 4 10 Running QSite Jobs 4 11 Calculating Properties ist e Fett e WEE Chapter 5 Running QSite from the Command Line La e en tea errr es enter 5 2 The qsite et ul ME 5 3 The QSite Input File nan 5 3 1 Additions to hegen Sektion ur sosse ea ae 5 3 2 The GMregion seclon null 513 3 elle Chapter 6 QSite Technical Notes nasse nes 6 1 QM MM for Protein Active Gites 6 2 QM MM Transition State Modeling AAA 6 3 How QSite Works QSite 5 0 User Manual Contents 6 4 Parametrization Validation 59 6 4 T Deprotonation Gre E 59 6 4 2 Gonformational Energies mus 60 6 4 3 Other Comparisons ns ln rail 60 6 5 An Illustrative Application 61 6 6 Le 62 Getting TA N OR 65 EN EE 67
29. If help is available for the task you are performing it is automatically displayed there Auto Help contains a single line of information For more detailed information use the online help e If you want information about a GUI element such as a button or option there may be Balloon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Help menu of the main win dow If there is Balloon Help for the element it appears within a few seconds e For information about a panel or the tab that is displayed in a panel click the Help button in the panel The help topic is displayed in your browser e For other information in the online help open the default help topic by choosing Help from the Help menu on the main menu bar or by pressing CTRL H This topic is dis played in your browser You can navigate to topics in the navigation bar If you do not find the information you need in the Maestro help system check the following sources Maestro User Manual for detailed information on using Maestro Maestro Command Reference Manual for information on Maestro commands e Maestro Overview for an overview of the main features of Maestro e Maestro Tutorial for a tutorial introduction to basic Maestro features e Jaguar User Manual for information on Jaguar and its keywords e Impact Command Reference Manual for information on Impact commands e QSite Frequent
30. M internal coordinate 33 continuum solvation oe conventions document vil convergence criteria energy minimization 36 53 covalently bound ligands ssssssssseseeeeeeeeeeeeee 26 cutoffs non bonded cuts frozen orbital definition 21 hydrogen cap nenn 22 D dielectric Constant 28 52 directory installation 1 Maestro Working 2 distance dependent dielectriC 28 52 E electron density surface 39 electrostatic potential surface 39 electrostatic treatment 28 hydrogen CAPS sssssssssisessrssorsnonssisnerser 24 50 energy minimization 39 3133 convergence criteria 36 53 cycles maximum 35 53 Step SIZE sirina rizses 39 33 Steric Clashes in 35 entries merging for QSite oes 19 environment variable SCHRODINGER 1 3 F force field OPLS22001 re 2 ee 21 28 OPES 200S E 28 frozen EE 31 33 G geometry optimization sssssssssssssessnerensrsrsrnrn 37 H hydrogen bonds resolving clashes 16 hydrogen E 22 electrostatic treatment 24 50 specifying in GUI ssssessseeeererereerersrsrsese 26 specifying in input file 51 l identical CHATS ss someneenlitne 14 initial guess transition state calculation 39 MPUERIES eri nern restart J Januar sinne i 19 KEY WOTS s sccsscsssssssssssssssesse sss
31. OPLS_2001 and OPLS_2005 The default force field is OPLS_2005 Electrostatic treatment This option menu offers two methods for calculating the electrostatic component of the molec ular mechanics energy e Constant dielectric This option calculates the electrostatic interaction between atoms i and j as Ege 332 063762 giq r A constant dielectric is appropriate for a vacuum gas phase calculation or when an explicit or implicit solvent model is used Distance dependent dielectric This option calculates the electrostatic interaction between atoms i and j as Es 332 063762 q g e ri A distance dependent dielectric is sometimes used as a primitive model for the effect of solvent In this model the electrostatic interaction between a pair of atoms falls off rap idly as the distance between the atoms increases Continuum and explicit solvent models are much better at accounting for solvent effects than a distance dependent dielectric QSite 5 0 User Manual Chapter 4 Running QSite From Maestro AEE QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Force field OPLS_2005 Electrostatic treatment Constant dielectric Dielectric constant 1 0 W Use non bonded cutoffs Settings W Use continuum solvation Settings 1 Use atomic partial charges in structure file 1 Skip force field checks may be needed if metals are present
32. QSite 5 0 User Manual O Schr dinger Press QSite User Manual Copyright 2008 Schr dinger LLC All rights reserved While care has been taken in the preparation of this publication Schr dinger assumes no responsibility for errors or omissions or for damages resulting from the use of the information contained herein Canvas CombiGlide ConfGen Epik Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime PrimeX QikProp QikFit QikSim QSite SiteMap Strike and WaterMap are trademarks of Schr dinger LLC Schr dinger and MacroModel are registered trademarks of Schr dinger LLC MCPRO is a trademark of William L Jorgensen Desmond is a trademark of D E Shaw Research Desmond is used with the permission of D E Shaw Research All rights reserved This publication may contain the trademarks of other companies Schr dinger software includes software and libraries provided by third parties For details of the copyrights and terms and conditions associated with such included third party software see the Legal Notices for Third Party Software in your product installation at SSCHRODINGER docs htmi third_party_legal htmi Linux OS or SCHRODINGER docs html third_party_legal htmi Windows OS This publication may refer to other third party software not included in or with Schr dinger software such other third party software and provide links to third party Web sites linked sites References to such o
33. The table columns are e Coordinate Atom numbers of the atoms that define the coordinate e Type Coordinate type from the Type option menu Steps Number of steps to take in the given coordinate Calculated from the values pro vided in the Selected Coordinate section The total number of structures to be calculated is reported below the table and is the product of the numbers in the Steps column To set up the range for a coordinate 1 Select the coordinate in the Defined coordinates table 2 Enter values in the text boxes in the Selected coordinate section QSite 5 0 User Manual Chapter 4 Running QSite From Maestro In the Selected Coordinate section you can set the range of the scan and the spacing of the points along the scan coordinate for the coordinate that is selected in the table These values are used to calculate the number of steps The text boxes are described below e Current value Current value of the coordinate in the input structure Noneditable e Starting value Initial value of the coordinate for the scan Final value Final value of the coordinate for the scan e Increment Amount by which the coordinate is incremented at each scan step Number of steps Number of steps to take in the given coordinate Calculated from the initial and final values and the increment You can delete coordinates by selecting them in the table and clicking Delete in the Selected coordinate section
34. This residue is mostly in the QM region and the cut is made between N and Ca Frozen Error Peptide Peptide orb H kcal MM Region QM Region dist A mole ace ala L EU nma Hl 4 1 0 70 ace ala L EU nma H2 4 3 0 52 ace ala L EU nma H3 4 3 0 53 ace ala A LA leu nma Hl 5 2 0 40 ace ala A LA leu nma H2 5 5 0 34 ace ala A LA leu nma H3 6 3 0 29 ace ala A LA ala leu nma H1 8 7 0 20 ace ala A LA ala leu nma H2 9 7 0 15 ace ala A LA ala leu nma H3 8 2 0 23 ace ala ala ala ala ala L EU ala nma Hi 4 1 1 21 ace ala ala ala ala ala L EU ala nma H1 4 3 0 93 ace ala ala ala ala ala L EU ala nma H1 4 3 0 82 QSite 5 0 User Manual 59 Chapter 6 QSite Technical Notes 60 6 4 2 Conformational Energies Conformational energies afford a second critical test of the quality of the QM MM method ology Table 6 2 summarizes the RMS deviations between the QM MM or MM OPLS AA and the purely QM results for the relative energetics of the side chain rotamer data set used to parameterize QSite The QM MM results generally are at least as good as those from the OPLS AA force field and in many cases are much better The QM MM rotamer structures also display good fidelity to the QM structures 6 4 3 Other Comparisons QSite has also been shown to accurately reproduce patterns in quantum mechanical
35. acility requires an identified ligand 2 Simplify multimeric complexes For computational efficiency it is desirable to keep the number of atoms in the complex structure to a minimum If the binding interaction of interest takes place within a single subunit you should retain only one ligand receptor subunit to prepare for QSite If two identical chains are both required to form the active site neither should be deleted e Determine whether the protein ligand complex is a dimer or other multimer con taining duplicate binding sites and duplicate chains that are redundant e Ifthe structure is a multimer with duplicate binding sites remove redundant binding sites and the associated chains by picking and deleting molecules or chains 3 Locate any waters you want to keep then delete all others These waters are identified by the oxygen atom and usually do not have hydrogens attached Generally all waters except those coordinated to metals are deleted but waters that bridge between the ligand and the protein are sometimes retained If waters are kept hydrogens will be added to them by the preparation component of the protein preparation job Afterwards check that these water molecules are correctly oriented 4 Adjust the protein metal ions and cofactors Problems in the PDB protein structure may need to be repaired before it can be used Incomplete residues are the most common errors but may be relatively harmless if they are d
36. an color indicates that the row for this cut is selected in the table QSite 5 0 User Manual Chapter 2 QSite Tutorial BAE QM settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Method DFT B3LYP 1 Spin unrestricted Charge 0 Multiplicity 1 QM options jacc 1 vshift 1 0 maxit 100 wf QM Region OM Basis Type Name M Pick Free ligandion ligand ion 2 W Show markers Delete Delete All Update QM Region Display Total number of atoms in QM region 16 Start Read Write Close Help Figure 2 2 The QM Settings tab with the ligand picked QM region size is the most influential factor in QSite calculation speed It is therefore not advantageous to work with smaller model proteins 2 7 Running the QSite Job 1 In the lower left corner of the QSite panel click Start The QSite Start dialog box is displayed 2 Change the job name to gsite tutorial 3 Click Start The Monitor panel opens and displays the job log as it runs 4 Close the QSite panel This job runs for several hours If you wish to examine the results without waiting for the job to finish you may simply import the output structure file qsite 1tpb 01 mae from your working directory QSite 5 0 User Manual 7 Chapter 2 QSite Tutorial QSite Start Figure 2 3 The QSite Start dialog box The foll
37. apply Error in handling of full CT SIMPACT I foldmain calling opls2001 atomtyping SIMPACT I foldmain parameter assignment not performed SIMPACT E die At line 9 IMPACT E CREATE Molecule unsuitable for current force field To process this molecule you must first fix the structure then you should select Skip force field checks in the Potential tab or set notestff 1 in the mmkey section of your input file and rerun the job Note that these warnings or errors could also mean that there really is a problem with your structure which you should fix For example some atoms may have atom types that are incon sistent with their connectivity or formal charge or there may be atoms that are superimposed QSite 5 0 User Manual 45 46 QSite 5 0 User Manual Chapter 5 Running QSite from the Command Line Although you will normally set up QSite jobs using the controls and settings in the Maestro GUI you can submit jobs either from Maestro or from the command line The same is true for the Protein Preparation facility Advantages of running from the command line include e The command line scripts can run all full featured jobs written using the QSite and Impact panels in Maestro and also allow you to override specific run time values that are not accessible through the Maestro interface e Command line scripts allow you to run jobs when you want e Command line scripts can be modified and jobs can be r
38. arked with a purple cube After picking the second atom all of the backbone and side chain atoms between the two cuts are marked in sienna if Show markers is selected If you click twice on the same atom in an amino acid residue then the QM MM cuts will be set as small as possible so as to place that entire residue in the QM region Backbone cuts can be made in any peptide residue including glycine proline and their adjacent residues and including positively charged histidine HIP There is one excep tion backbone cuts on PRO residues cannot be made between the N atom and the Ca atom There must be at least 3 bonds between pairs of QM MM cuts that are made along the protein backbone This ensures that the QM MM boundaries are kept far enough apart that they do not interfere with one another This means that the smallest QM region that contains all of the atoms of an amino acid residue would necessarily contain an extra car bonyl group and an extra N H bond from the neighboring residues QSite 5 0 User Manual 25 Chapter 4 Running QSite From Maestro 26 A backbone cut cannot be placed between an amino acid residue and an end cap The end cap must be included in the QM region To do this you may click on any atom in an end cap and on any other atom in an amino acid residue further up the chain In this case only one cut will actually be made and all atoms from the cut to the end of the chain will be placed into the QM regio
39. ch forces are considered long range and are therefore updated every n steps for Truncated Newton minimizations in this text box The default value is 10 0 4 7 The QM Optimization Tab The QM Optimization tab specifies the type of QM Jaguar calculation to be performed and provides information needed to set up the calculation For transition state optimizations addi tional structures reactant product and transition state guess structures can be given to guide the search QSite geometry optimizations use internal coordinates by default to force Carte sian coordinate optimization run QSite from the command line using the option intopt 0 in the gen section of the Jaguar input file The options available in this tab are described in the following sections 4 7 1 Calculation Type The Method menu controls the QM calculation type The options are e Single point Calculate the QM energy for the structure as it stands No QM geometry optimization or MM minimization is performed When Single point is selected other options in this tab are unavailable Settings in the Minimization and Constraints tabs are ignored This is the default QM method e Minimization Locate a minimum energy structure by geometry optimization If you want to optimize only the QM region simply set the number of minimization steps to 0 in the Minimization tab There is no need to explicitly freeze all of the MM atoms e Transition state Locate a transition stat
40. d by the atom name and an underscore Must be given with hcapmm hcapmm MM atom for cuts made by the hydrogen cap link atom method The atom can be specified by the Maestro atom number optionally prefixed by the atom name and an underscore Must be given with hcapqm amp qmregion molid chain resnum qmatom mmatom 2 A 455a CA N 2 A 277 CA 2 B 1211 CB CA molid 7 qmatom 774 0_422 qnatom mmatom 237 238 N_222 C_1285 hcapqm hcapmm 852 853 C_125 C_61 amp The first two specification lines in the example above describe backbone cuts The third is a side chain cut and the fourth specifies an entire molecule The fifth specification line is equiv alent to the fourth gsite follows the connectivity from the atom indicated until the connec tivity run s out The next two specification lines can be used to specify the locations of cuts QSite 5 0 User Manual 51 Chapter 5 Running QSite from the Command Line 52 which may not be in amino acid residues This syntax could be used for nucleic acid cuts for example although the first syntax would also work for amino acid cuts For generalized cuts Maestro atom numbers are the only way to define the location of a cut The last two specifica tion lines define hydrogen caps 5 3 3 The mmkey Section The mmkey section includes keywords for specifying the MM potential corresponding to choices in the Potential tab of the QSite panel for controlling the MM minimization MM Mi
41. e run without reconfiguring and reloading job settings in Maestro e Some job options are available only when you run QSite from the command line The SCHRODINGER environment variable must be set to run jobs You can define SCHRODINGER as follows csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory Unless otherwise specified Schr dinger applications and utilities run under the Schr dinger Job Control facility and are automatically run in the background For more information on the Job Control facility see the Job Control Guide 5 1 QSite Files QSite jobs have a single input file which is like the Jaguar input file The input for the QM part of the calculation is included as regular Jaguar sections with their keywords The input for the MM part is embedded in an mmkey section and consists of keywords that correspond to the Impact commands The QM region is defined in a separate qmregion section The Write button in the QSite panel writes the input files needed for a job See Section 4 1 2 on page 20 for more information A typical QSite job has one input file jobname in one or more structure files jobname mae Jobname pdb or jobname sdf and after execution several output files Table 5 1 contains descriptions of the various file types QSite 5 0 User Manual 47 Chapter 5 Running QSite from the Command Line 48 Table 5 1 QSite input and output files
42. e structure by geometry optimization The remaining controls in the tab define the initial guess for the transition state geometry and are described in the next subsection For minimization and transition state calculations you can specify the number of optimization iterations in the Maximum number of iterations text box The default is 100 iterations QSite 5 0 User Manual 37 Chapter 4 Running QSite From Maestro 38 QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization Surfaces Scan Optimization options for the QM region Method Transition state Maximum number of iterations 100 TS method LST 1 Reactant entry Choose Pick to define entry Product entry Choose I Pick to define entry 0 50 TI Fraction of path between reactant and product Start Read Write Close Help Figure 4 8 The QM Optimization tab with TS method LST selected 4 7 2 Transition State Searches If you select Transition state from the Method menu the default option for TS method is Stan dard The following three methods for transition state optimization are supported in QSite corresponding to well known ab initio techniques See Section 4 3 of the Jaguar User Manual for detailed information about these methods e Standard The standard transition state optimization method is useful if you have only a single initial guess str
43. ed location and to enter text means to type the required text then press the ENTER key References to literature sources are given in square brackets like this 10 QSite 5 0 User Manual viii QSite 5 0 User Manual Chapter 1 Introduction 1 1 About QSite QSite is a mixed mode Quantum Mechanics Molecular Mechanics QM MM program used to study geometries and energies of structures not parameterized for use with molecular mechanics such as those that contain metals or represent transition states QSite is uniquely equipped to perform QM MM calculations because it combines the superior speed and power of Jaguar with the recognized accuracy of the OPLS AA force field Jaguar is used for the quantum mechanical part of the calculations and Impact provides the molecular mechanics simulation The Jaguar component can be run in parallel if multiple processors are available either from the command line or from the GUI QSite is run primarily from the Maestro graphical user interface A tutorial in using QSite from Maestro appears in Chapter 2 QSite can also be run from the command line as described in Chapter 5 Utilities and scripts are also run from the command line QSite is only available on UNIX platforms Maestro is Schr dinger s powerful unified multi platform graphical user interface GUD It is designed to simplify modeling tasks such as molecule building and data analysis and also to facilitate the setup and submi
44. eme button menu ay A ft Each of the four molecules in the Workspace two receptors and two ligands is now dis tinctly colored and you can see what changes have occurred in the optimization 4 Choose Element from the Color all atoms by scheme toolbar button menu ay A Corresponding atoms in the two entries are now colored identically 2 8 2 Comparing Ligand Receptor Interactions In this exercise you will compare the hydrogen bonding interactions between ligand and receptor in the input complex and the output complex 1 Include only the input entry in the Workspace 2 Choose Inter H Bonds from the Display H bonds toolbar button menu H A QSite 5 0 User Manual 9 Chapter 2 QSite Tutorial 10 Figure 2 5 Output structure ligand receptor hydrogen bonds QSite 5 0 User Manual Chapter 2 QSite Tutorial 3 Pick the ligand molecule Hydrogen bonds between the ligand and nearby receptor residues are shown as dashed yellow lines as shown in Figure 2 4 4 Control click the In check box for the output entry Both entries are now included 5 Control click the In check box for the input entry to exclude it Using control click to include and exclude entries allows the definitions of the molecules to display H Bonds for to stay the same In the output structure notice that the hydrogen bond between LYS 13 and the ligand has been lost while two new hydrogen bonds have formed between ASP 16
45. es angles and dihedrals and set Cartesian constraints These constraints freeze the internal or Cartesian coordinates For Cartesian coordinates you can only freeze the entire atom not indi vidual coordinates You can also make constraints dynamic which means that the optimization will constrain the parameter to reach the target value specified at convergence Harmonic constraints are not available in the QSite panel but can be set by using Jaguar keywords QSite 5 0 User Manual 33 Chapter 4 Running QSite From Maestro 34 QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Add new constraint Type Angle T Pick Atoms Constraints 1856 1857 1861 Selected constraint 108 000000 13 E Dynamic Target value 108 d Delete Delete All Start Read Write Close Help Figure 4 6 The QM Constraints tab of the QSite panel To set a constraint choose the parameter type from the Type menu select Pick if it is not already selected choose Atoms or Bonds from the Pick menu then pick the atoms in the Workspace for the constraint The constraints are marked in the Workspace with a spring icon and lines to indicate the atoms involved and the type of constraint To make a constraint in the Constraints table dynamic select the table row then select Dynamic in the Selected cons
46. he chemistry of ligand binding of cytochrome P450 with conven tional molecular modeling techniques The existence of a reactive metal center and the centrality of the reactive chemistry in the interaction of the enzyme with various drug candi dates mandate a quantum chemical treatment of the active site On the other hand the protein structure is clearly important in selectivity binding affinity and reaction kinetics and cannot be incorporated to any great degree with conventional quantum chemical techniques QSite is well suited to addressing this problem with relatively modest computational resources Its application to a problem in cytochrome P450 chemistry 6 is recounted below 1 Structure and QM Region The particular systems studied are available as entries Iphf and 1akd in the PDB archives The former has a coordinating phenylimidazole ligand while the latter is the so called substrate free state with a non coordinating camphor ligand located near the heme 2 P 450 and Phenylimidazole Ligand The 1phf structure has a 4 phenylimidazole complexed with Fe On the opposite side of the heme Fe is coordinated to a cysteinate sulfur R S7 Thus the Fe is in a six fold coordination site and is assumed to be Fe given the S formal charge and the two nega tive charges distributed over the four coordinating nitrogens in the heme ring system The net spin state is either a doublet with the Fe S moiety low spin coupled as in the coordi
47. his optimizer does not make large scale changes the partial minimization can be done even on the isolated ligand or protein without danger of altering the conformation significantly However if comparison to the orig inal complex shows that the electrostatic mismatch due to the misprotonation has appreciably changed the positions of the ligand or protein atoms during the protein preparation procedure it is best to reprotonate the original structure and redo the restrained minimization QSite 5 0 User Manual 17 18 QSite 5 0 User Manual Chapter 4 Running QSite From Maestro QSite performs mixed quantum mechanical molecular mechanical QM MM calculations using Jaguar for the QM calculations and Impact for the MM calculations Ligands and other specified regions of a protein complex can be studied using QM while MM is used for the rest of the molecule At each step of a QM geometry optimization Impact calculates energy terms for MM QM region interactions if MM minimization was also specified it is also performed at each QM step The next QM step takes into account the new MM atom distribution and energy terms If a single point QM calculation is selected the current QM MM energy is calculated without MM minimization The speed of QSite is largely determined by the size of the QM region Therefore there is no advantage to making a smaller model protein You can run calculations on systems with up to than 8000 atoms or 8000 bonds f
48. ile name for the first job it is jobname 01 mae The index number is the same as for the restart file QSite 5 0 User Manual 43 Chapter 4 Running QSite From Maestro 44 To restart a job from Maestro open the QSite panel and click Read A file selector opens in which you can navigate to and select the restart file When you click OK the structure is imported as well as the settings You can select options in the QM Settings tab to read the wave function and the Hessian from the input file You can then click Start to open the Start dialog box to restart the job 4 11 Calculating Properties In addition to the calculation of surfaces described in Section 4 8 on page 39 vibrational frequencies NMR shielding constants and molecular polarizabilities can be calculated for the QM atoms when the QM region is defined using hydrogen caps or when the QM region consists of one or more noncovalently bound ligands i e no frozen orbital cuts or hydrogen caps To calculate these properties you must add the relevant keywords to the gen section of the input file You can do this in the QM options text box in the QM Settings tab or you can edit the input file For information on the relevant keywords see Section 8 5 14 of the Jaguar User Manual Note Properties for atoms that are within a few bonds of frozen orbital cuts or hydrogen caps are likely to be unreliable and should be treated with caution This is because the representat
49. inate scan Whether the scan is relaxed or rigid depends on the method selection in the QM Optimization tab selecting Single point from the Method option menu performs a rigid scan selecting Minimization performs a relaxed scan To add a new scan coordinate 1 Choose a coordinate type from the Type option menu 2 Choose Atoms or Bonds from the Pick option menu 3 Pick the atoms or bonds in the Workspace The order of picking of the coordinates determines which atoms are moved in the scan the last atom picked is the moving atom and the first atom picked remains stationary If you are picking bonds they must be contiguous The last atom the moving atom is the atom in the last bond picked that is not part of the previous bond picked The choice you make from the Type option menu determines the number of atoms to pick The Z matrix must be in the appropriate form for the coordinate type Cartesian for Cartesian coor dinates and Z matrix for distances angles and dihedrals The coordinate types are e Cartesian X X coordinate of an atom Pick one atom e Cartesian Y Y coordinate of an atom Pick one atom e Cartesian Z Z coordinate of an atom Pick one atom e Distance Distance between two atoms Pick two atoms or one bond If you pick atoms they need not be bonded to each other e Angle Angle between three atoms Pick three atoms or two bonds If you pick atoms they need not be bonded to each other e Dihedral Dihedral a
50. ion of the wave function near the cuts does not accurately represent the wave function of the full system 4 12 Troubleshooting This section contains information on various conditions that you might encounter and offers some suggestions to work around or fix the problems mmlewis warnings or atom typing failures By default Impact performs a number of tests during atom typing to guide selection of optimal force field parameters for the atoms in the input structure The tests are applied to both the MM and the QM regions For transition metals force field parameters are more limited than for the common p block elements so when the structure contains transition metals these atom typing tests can fail and cause the job to halt If this happens you can select Skip force field checks in the Potential tab or add the setting notestff 1 to the mmkey section of your input file and rerun the job from the command line The notestff 1 setting directs Impact to skip the extra atom typing tests and this may allow your job to run Specifically if there are metal atoms in your structure and you see warnings like mmlewis warning Problems were identified with the following atoms mmlewis warning 4471 4476 QSite 5 0 User Manual Chapter 4 Running QSite From Maestro mmlewis warning Now attempting to fix the lewis structure or if your job halts with this error Impact FATAL mmlewis apply Unable to handle mol 9 Impact FATAL mmlewis
51. is option to pick the location of one or more cuts and choose the type of cut from the option menu Note that a residue can be an amino acid residue a free ligand or solvent mole cule or an ion The items on the option menu are e Side chain Choose this option to add only the side chain of an amino acid residue to the QM region leaving the backbone in the MM region Pick an atom in the side chain you want to include The side chain is marked in sienna if Show markers is selected A cut is made between the alpha carbon and the beta carbon of that residue All of the atoms in the side chain are part of the QM region Side chain cuts can be made in any peptide residue other than alanine ALA glycine GLY and proline PRO To incorporate side chains from these residues in the QM region you must select the entire residue by using a backbone cut Side chain cuts can be made in positively charged histidine HIP as well Side chain cuts are not permitted if the side chain has been modified within 3 atoms of the alpha carbon atom Entire residue To add entire amino acid residues to the QM region choose this option and then pick two atoms that are not alpha carbons and are at least three backbone bonds apart The residues containing these two atoms and the residues in between are included in the QM region The cut between MM and QM atoms is made between the alpha carbon and the backbone atom bonded to it When you pick the first atom it is m
52. istant from the active site Structures that are missing residues near the active site should be repaired For the MM calculations metal ions in the protein complex cannot have covalent bonds to protein atoms The MacroModel atom types for metal ions are sometimes incorrectly translated into dummy atom types Du Z0 or 00 when metal protein bonds are specified in the input structure Furthermore isolated metal ions may erroneously be assigned gen eral atom types GA GB GC etc Cofactors are included as part of the protein but because they are not standard residues it is sometimes necessary to use Maestro s structure editing capabilities to ensure that mul tiple bonds and formal charges are assigned correctly Fix any serious errors in the protein QSite 5 0 User Manual Chapter 3 Protein Preparation e Check the protein structure for metal ions and cofactors e If there are bonds to metal ions delete the bonds then adjust the formal charges of the atoms that were attached to the metal as well as the metal itself e Set charges and correct atom types for any metal atoms as needed e Set bond orders and formal charges for any cofactors as needed 5 Adjust the ligand bond orders and formal charges If the complex structure contains bonds from the ligand or a cofactor to a protein metal they must be deleted Impact models such interactions as van der Waals plus electrostatic interactions Impact cannot handle norma
53. l covalent bonds to the ligand such as might be found in an acyl enzyme If you are working with a dimeric or large protein and two ligands exist in two active sites the bond orders have to be corrected in both ligand structures 6 Run a restrained minimization of the protein structure This is done with impref and should reorient side chain hydroxyl groups and alleviate potential steric clashes 7 Review the prepared structures e If problems arise during the restrained minimization review the log file correct the problems and rerun Examine the refined ligand protein water structure for correct formal charges bond orders and protonation states and make final adjustments as needed 3 2 Checking the Protein Structures After you have completed the protein preparation you should check the completed ligand and protein structures 3 2 1 Checking the Orientation of Water Molecules You only need to perform this step if you kept some structural waters Reorienting the hydro gens is not strictly necessary as their orientation should have been changed during refinement but it is useful to check that the orientation is correct If the orientation is incorrect reorient the molecules by using the procedure outlined in Section 3 9 of the Protein Preparation Guide When you have corrected the orientation of the retained water molecules you should run a refinement on the adjusted protein ligand complex QSite 5 0 User Manual
54. ly Asked Questions pages at https www schrodinger com QSite FAQ html QSite 5 0 User Manual 65 Getting Help 66 The manuals are also available in PDF format from the Schr dinger Support Center Informa tion on additions and corrections to the manuals is available from this web page If you have questions that are not answered from any of the above sources contact Schr dinger using the information below E mail help schrodinger com USPS Schr dinger 101 SW Main Street Suite 1300 Portland OR 97204 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Generally e mail correspondence is best because you can send machine output if necessary When sending e mail messages please include the following information e All relevant user input and machine output e QSite purchaser company research institution or individual e Primary QSite user e Computer platform type e Operating system with version number QSite version number e Maestro version number e mmshare version number On UNIX you can obtain the machine and system information listed above by entering the following command at a shell prompt SSCHRODINGER utilities postmortem This command generates a file named username host schrodinger tar gz which you should send to help schrodinger com If you have a job that failed enter the following command SCHRODINGER utilities postmorte
55. m jobid where jobid is the job ID of the failed job which you can find in the Monitor panel This command archives job information as well as the machine and system information and includes input and output files but not structure files If you have sensitive data in the job launch directory you should move those files to another location first The archive is named Jobid archive tar gz and should be sent to help schrodinger com instead More information on the postmortem command can be found in Appendix A of the Job Control Guide QSite 5 0 User Manual A algorithms seeiis 35 39 MM energy minimization 35 23 transition state search eeeeeeeeeeeeee 38 atom constraints oi atom typing failures ssssesessrsrssrsrsrsersrsrsrerrsrenr 44 atoms choosing basis set for 27 constrained susanne asien 31 33 TING Avi dess E nte sen sense 26 B backbone cuts restrictions on 25 backbone leaving in MM region e basis set for QM region 27 C Cartesian coordinates MM CONStr ln S 5 s ssissssoess ssassassrnsorsnnsnesses 31 Optimization Of 37 QM constraints oossnssssssessesrsrsrrsrsrsrrsrsrsnerrsr ert 33 CLOSE Contacts ie enter ren 16 constant dielectric eeenenenenennen 28 Constrained Atoms panel 33 constraints Cartesian wisalinhunkdueadendukads 31 33 E en hed Has 33 34 frozen atom 31 33 harmonic 31 33 Q
56. n The cuts made with this choice use the frozen orbitals method for defining the terminus of the QM region Free ligand ions Entire free ligands metal ions or other species not covalently bound to the protein can be added to the QM region by this method which does not make any cuts between atoms Select this option then pick a metal ion or an atom in the ligand molecule to add it to the QM region Molecules are marked in sienna and single atoms or ions are marked in cyan if Show markers is selected Ligands that are covalently bound to the protein cannot be added using this method because this method does not make parametrized cuts between bonded atoms To add covalently bound ligands to the QM region make either a pair of backbone cuts to select the residue to which the ligand is bound or make a side chain cut e Hydrogen cap To define cuts that are capped by hydrogen atoms rather than atoms with frozen orbitals select this option and then pick the QM atom followed by the MM atom on either side of the cut The QM atom and the MM atom must be joined by a single bond The MM atom is replaced by a hydrogen atom in the QM calculation The QM region usually requires two or more cuts The markers in the Workspace are not updated after making this kind of cut Instead you must click Update QM Region Display to display the markers for the QM region provided Show markers is selected Once you have created a hydrogen cap the Hydroge
57. n Keyword Value Description solvation method use mae charges use nb cutoff pbf 011 011 Solvation method turns on solvation and chooses the solvation model Default not present Use atomic partial charges from the input struc ture Maestro file if set to 1 If set to 0 the force field is used to determine the atomic partial charges Only use when the QM region consists of one or more non covalently bound molecules see page 31 for details Default 0 Use non bonded cutoffs Default 1 Table 5 7 Keywords for MM minimization in the mmkey section Keyword Values Description init_step_size rms_gradient converge_on deltae max_step_size maxcycles opt_method tn_force_cutoff tn_force_update real number real number energy I gradient eandg real number real number integer conjugate steepest tnewton real number integer Initial step size Default 0 05 Gradient threshold Default 0 01 Specify quantities that will be tested for conver gence energy gradient or both Default eandg Energy change threshold Default 0 1 Maximum step size Default 1 0 Maximum number of minimization cycles If zero no minimization is performed Default 1000 Optimization algorithm The three choices are conjugate gradient steepest descent and trun cated Newton Default conjugate Long range force cutoff Default 10 0 Interval between long range fo
58. n sional torsional profiles were generated at the same level of theory for all minima and relevant torsional degrees of freedom 2000 QM data points in all Alanine tetrapeptide conforma tions generated via the same protocol were used to test transferability In addition a database consisting of hydrogen bonded pairs of small molecule side chain analogues was constructed About 200 such pairs were used to determine van der Waals radii for QM atoms that yield accurate hydrogen bonding energetics between QM and MM donors and acceptors These data sets are considerably more extensive and of higher quality than any that have been used previ ously in developing or testing QM MM models of peptides and proteins Both DFT and Hartree Fock parameter sets have been developed The LMP2 version of the theory has been implemented for use in single point calculations It has not yet been fully parameterized but can be used to compare structures and energies when there is little change in the protein geometry in the vicinity of the frozen orbital interfaces Details of the parameter optimization methodology are provided in the previously cited references QSite makes use of a tight coupling between Jaguar and Impact Key features of the implemen tation are as follows QSite adiabatically minimizes the MM region after each QM geometry step Without this the number of QM steps would become prohibitively large and would place the cal culations out
59. n cap electrostatics option menu in the general section becomes available and you can choose the electrostatic treatment of MM atoms near the cap Show markers option If this option is selected markers are displayed in the Workspace to indicate the QM region Ball and stick markers are superimposed on the QM region atoms The markers are colored sienna The markers that correspond to the selected rows in the QM region table are colored cyan For hydrogen caps an arrow is superimposed on the bond where the cap will be placed pointing to the MM atom that will be replaced with a hydrogen atom QSite 5 0 User Manual Chapter 4 Running QSite From Maestro BAE QM settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Method DFT B3LYP 1 Spin unrestricted Charge 0 Multiplicity 1 QM options jacc 1 vshift 1 0 maxit 100 LJ FF Pick Atom E A W Show markers Basis set lacvp Update QM Region Display Total number of atoms in QM region 31 Start Read Write Close Help Figure 4 2 The QM Settings tab of the QSite panel showing the QM Basis subtab 4 2 3 QM Basis subtab In this subtab you can view and change the basis set associated with each atom in the QM region Basis set table This table lists the basis set used for each QM atom The atom is identified in the QM Atom
60. n will halt with an error message The charge and multiplicity of the QM region must be mutually consistent By default open shell calculations are spin restricted If you want to perform a spin unrestricted HF or DFT calculation you can select the Spin unrestricted option QM options This text box can contain any Jaguar keywords such as print settings non default convergence criteria and so on Each such option is of the form keyword value with no embedded blanks Multiple keyword value pairs can be specified separated by one or more blank spaces By default the following QM options appear in the box iacc 1 vshift 1 0 maxit 100 You can remove or modify these options as appropriate See Chapter 8 of the Jaguar User Manual for more information on Jaguar keywords QSite 5 0 User Manual 23 Chapter 4 Running QSite From Maestro 24 Hydrogen cap electrostatics This option menu allows you to choose how atoms in the MM region in the vicinity of a hydrogen cap are treated when calculating their electrostatic interaction with the QM region It is only available when you are using hydrogen caps to define part or all of the QM region e Point charges Use modified point charges to represent the potential of the atoms near the cap and MM point charges for the rest of the MM region e Gaussian charges Use Gaussian charge distributions to represent the potential of the atoms near the cap and MM point charges for the rest of
61. nated dioxygen state of P 450 or a high spin quartet There are 7075 atoms in the system The QM region is the full heme ring the Fe the full coordinating cysteine residue includ ing residues on either side of the cysteine and the 4 phenylimidazole The two QM MM cuts were made in the residues adjacent to the coordinating cysteine The net charge of the QM region is 2 from the two carboxylate groups on the heme There are 125 total quantum atoms and 1138 6 31G basis functions The QM method used was B3LYP DFT The outer shell of the protein was frozen during the optimization leaving 3960 of the 7075 atoms free to optimize This procedure is commonly used to avoid irrelevant energy differences caused by re arrangements of the outer parts of the protein QSite 5 0 User Manual 61 Chapter 6 QSite Technical Notes 62 3 P 450 and Camphor The specification of this system 1akd is identical to that above but with a quantum cam phor molecule replacing the phenylimidazole ligand The camphor is not directly bound to the Fe but like the phenylimidazole ligand has forced water out of the heme binding region The main purpose of running this system was to find the lowest spin state of the substrate free P 450 Preliminary results The P 450 optimization was run on 6 SGI R10000 nodes in about a 1 week of wall clock time The calculation took 30 QM MM geometry optimization cycles Approximately 10 hours was spent on the initial
62. nded interactions Click Settings to open the Truncation panel There are two settings that can be changed e Update neighbor list frequency steps The number of steps after which the neighbor list will be updated The default is 10 steps in the MM part of the calculation Larger values will speed up the calculation at the possible expense of accuracy e Residue based cutoff distance All atoms in complete residues that have any pair of atoms within this distance are included in the nonbonded interaction list The default is 12 A This value should be increased to avoid convergence problems to a value like 30 A Smaller values will speed up the calculations but could miss important long range electrostatic interactions between formally charged atoms This option affects both MM and QM calculations Do not select Use continuum solvation if you intend to run the QM Jaguar calculation using multiple processors parallel processing when QSite jobs with solvation are run in parallel erroneous energies result If you want to use explicit water solvent rather than continuum solvation you can add the water molecules using the Soak application of Basic Impact followed by an equilibration also using Basic Impact See Chapter 5 of the Impact User Manual for more information on Soak Use continuum solvation Select this option and click Settings to open the Continuum Solvation dialog box The only available solvation method in QSite for both
63. ngle between four atoms Pick four atoms or three bonds If you pick atoms they need not be bonded to each other The choices available on the Pick option menu are Atom for Cartesian coordinates and Atom and Bond for all other types of coordinates The atoms are marked in the Workspace as you pick them and each coordinate is marked in the Workspace and entered in the Defined coordi nates table as it is completed If you want to select a protein dihedral angle click Select A dialog box is displayed in which you can select a standard dihedral from a list 7 Sets plotres in the gen section QSite 5 0 User Manual 41 42 Chapter 4 Running QSite From Maestro QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces Scan Add new coordinate Type Distance Pr Pick Atoms 1 Gei Defined coordinates maximum of 5 Coordinate rype steps Selected coordinate 1856 1857 Distance T i Ze an Ze Current value 1 504 Starting value P 0 00 7 Final value 0 00 Total number of structures to be calculated 1 Increment 9 000 Number of steps 1 Delete Delete All Start Read Write Close Help Figure 4 10 The Scan tab The Defined Coordinates table displays information on the scan coordinates You can select a single row to define the range and point spacing for the coordinate in the Selected Coordinate section
64. ni mization tab and for constraints MM Constraints tab MM potential keywords are listed in Table 5 6 and MM minimization keywords are listed in Table 5 7 There is one keyword for constraints buf force const which is the force constant for constrained atoms and has a default value of 25 0 Detailed information about the parameters that are set can be found in Section 4 3 on page 28 and Section 4 6 on page 35 Table 5 6 Potential energy keywords for the mmkey section Keyword Value Description dielectric real number Dielectric constant Default 1 0 estatics nodist dist Electrostatic treatment use a constant nodist or a distance dependent dist dielectric Default nodist nb_cutoff_dist real number Residue based cutoff distance in angstroms Default 12 0 nb_update_freq integer Frequency with which the neighbor list is updated in steps Default 10 notestff 011 Turn off consistency checks notestff 1 when performing atom typing These checks can pre vent a valid structure from being accepted when the structure contains atoms in the QM region that are not recognized in the force field Default 0 pbf disp real number PBF displacement threshold Default 0 1 pbf resolution low l med I high PBF resolution Default low qsite_ff opls2001 op1s2005 Force field Default op1s2001 QSite 5 0 User Manual Chapter 5 Running QSite from the Command Line Table 5 6 Potential energy keywords for the mmkey sectio
65. nstallation_path sh bash ksh export SCHRODINGER installation_path 2 Change to a directory in which you have write permission 3 Create a new working directory by entering the command mkdir qsite workdir 4 Change to this new working directory and copy the QSite tutorial files to it cp SSCHRODINGER impact vversion tutorial qsite qsite 2 2 Starting Maestro You do not need to start Maestro until you begin the exercises If you have not started Maestro before this section contains instructions QSite 5 0 User Manual 3 Chapter 2 QSite Tutorial 1 Change to your qsite workdir directory 2 Enter the command SSCHRODINGER maestro amp The Maestro main window is displayed 2 3 Importing the Complex Use the following steps to import the protein ligand complex in the file gsite 1tpb mae 1 Click the Import structures toolbar button The Import panel is displayed Choose Maestro from the Format menu Navigate to gsite workdir if necessary and select the file gsite 1tpb mae Ensure that Replace Workspace is selected On A N Click Import The 1TPB receptor ligand complex is included in the Workspace This complex has already been prepared for use in QSite Normally you would need to prepare the complex using the Protein Preparation Wizard panel see Chapter 2 of the Protein Preparation Guide for more information 6 Click Close to close the Import panel 2 4 Setting Up the Display
66. nu QSite 5 0 User Manual 5 Chapter 2 QSite Tutorial QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Force field OPLS_2005 Electrostatic treatment Constant dielectric Dielectric constant 1 0 W Use non bonded cutoffs Settings W Use continuum solvation Settings 1 Use atomic partial charges in structure file 1 Skip force field checks may be needed if metals are present Start Read Write Close Help Figure 2 1 The Potential tab of the QSite panel 2 6 Defining aQM Region You can select an isolated ligand molecule a lone ion or a metallic cofactor for the QM region by simple picking To select entire residues from protein chains you must make backbone cuts or use hydrogen caps It is often useful to make side chain cuts adding only the side chain rather than the entire residue to the QM region The following exercise demonstrates QM region definition by ligand picking 1 In the QM Region subtab of the QM Settings tab ensure that the Pick option is selected 2 Choose Free ligand ion from the Pick option menu 3 Pick an atom in the ligand Markers in cyan are superimposed on the ligand molecule to indicate that it has been selected for the QM region In the table the type of cut and the name of the residue or ion are listed In this case the name is the molecule number The cy
67. o User Manual 1 3 Citing QSite in Publications The use of this product should be acknowledged in publications as QSite version 5 0 Schr dinger LLC New York NY 2008 QSite 5 0 User Manual Chapter 2 QSite Tutorial This chapter contains a tutorial designed to help you quickly become familiar with QSite using the Maestro interface In this chapter you will perform a QSite geometry minimization on a protein ligand complex Density functional theory DFT will be used to treat the QM region which will consist of the ligand only This is a straightforward example of using QSite to model a stationary state QSite can also be useful in modeling enzymatic systems involving transition states or metal atoms which can be poorly treated by empirical force fields To do these exercises you must have access to an installed version of Maestro 8 5 and QSite 5 0 For installation instructions see the Installation Guide 2 1 Preparing a Working Directory Files needed for this tutorial are included with the Impact distribution The SCHRODINGER impact vversion tutorial gsite directory contains the input files needed to begin this tutorial as well as the output files Before you start Maestro you must set the SCHRODINGER environment variable create a local working directory and copy the QSite tutorial files to it 1 Set the SCHRODINGER environment variable to the product installation directory csh tesh setenv SCHRODINGER i
68. o obtain chemically realistic results Hartree Fock HF density functional DFT and local MP2 LMP2 methods are available for the QM MM region although geometry optimization has been implemented only for the first two of these methods We have found DFT methods to be particularly useful for studying protein active site reactive chemistry QSite provides QM MM interface parameters for all 20 amino acids in their various protona tion states This ensures that you will be able to construct a QM region tailored specifically to your needs Maestro provides an easy and reliable way to set up the QM MM interface via pointing and clicking with the mouse on residues of the protein active site Protein preparation can be carried out using the procedure described in Chapter 3 This technology makes setting up a new QM MM job a task that can be carried out effectively and straightforwardly One key use of QSite is to study ligand binding to transition metal containing enzymes such as zinc matrix metalloproteases Conventional molecular mechanics force fields usually model ligand interactions with protein metals in a primitive fashion i e as a van der Waals body and a charge site Jaguar contains specialized methods for treating transition metals that include a novel initial guess methodology and variable energy shift algorithms to converge difficult QSite 5 0 User Manual 55 Chapter 6 QSite Technical Notes 56 cases The combination of Jag
69. of active site modeling applications QSite 5 0 User Manual Chapter 6 QSite Technical Notes 6 4 Parametrization Validation 6 4 1 Deprotonation Energies Chemical reaction energetics provide one important measure of how well a QM MM model reproduces accurate quantum mechanics Below we examine a simple reaction removal of a proton from the QM region Table 6 1 compares differences between the QM and QM MM deprotonation energies for the capped peptides we have examined and lists the distance between the proton to be removed and the frozen interface orbital When this distance is greater than 5 A a distance that one would want to maintain between a reactive chemical event and the QM MM interface in any event the error is less than 0 4 kcal mole This error is negligible when compared to total reaction energies of hundreds of kcal mole and is small even in comparison to the intrinsic error HF or DFT calculations make relative to experiment DFT does quite well with a large basis set but still makes errors on the order of 1 2 kcal mole for small molecule deprotonation energies When the reactive event is very close to the frozen bond the errors can be somewhat larger but are still very reasonable Table 6 1 B3 LYP 6 31G QM MM absolute deprotonation energy differences relative to fully QM B3 LYP 6 31G values denotes the deprotonated QM leucine residue H of C The line through the capitalized residue denotes the QM MM boundary
70. owing files appear in your current Maestro working directory gsite workdir before the job starts qsite_tutorial in QSite input file qsite_tutorial mae Maestro structure file When the job is complete these files are written qsite_tutorial out QSite output file qsite_tutorial log Log file as displayed in the Monitor panel qsite_tutorial 01 in QSite restart file qsite_tutorial 01 mae Maestro structure file with optimized structure 2 8 Examining Results In the next two exercises you will examine the results of the calculation If you decided not to run the job you can import the results from your working directory as follows 1 Click the Import structures toolbar button So The Import panel is displayed 2 Choose Maestro from the Format menu 3 Select the file qsite 1tpb 01 mae QSite 5 0 User Manual Chapter 2 QSite Tutorial 4 Ensure that Replace Workspace is selected 5 Click Import 2 8 1 Comparing Input and Output Structures 1 Click the Open Close project table toolbar button EH The Project Table panel opens The output structure has been appended to the project as an entry with properties QM MM Energy QM Basis QM Method and Job Name By default the output structure is included in the Workspace 2 Control click the check box in the In column for the original structure The original structure is included in the Workspace as well 3 Choose Molecule Number from the Color all atoms by sch
71. rce updates in steps Default 10 QSite 5 0 User Manual 53 54 QSite 5 0 User Manual Chapter 6 QSite Technical Notes The study of reactive chemistry in a protein environment is an extremely challenging problem for computational chemistry The only methods that can produce reliable results particularly for structures containing transition metals are those of ab initio quantum chemistry However such methods are computationally intensive and scale poorly N N for self consistent field based approaches such as density functional theory with the number of atoms N making it impractical to apply them to an entire protein An attractive solution is use a mixed quantum mechanics classical molecular mechanics QM MM method such as QSite Such methods treat the reactive core of the system quantum mechanically and model the remainder via a clas sical molecular mechanics force field 6 1 QM MM for Protein Active Sites QSite is specifically designed to treat protein active sites It combines Schr dinger s powerful Jaguar program for ab initio electronic structure calculation with molecular mechanics calcula tions that use the OPLS AA force fields of Jorgensen and coworkers The speed of Jaguar augmented by an MPI based parallel implementation makes it possible to study realistic representations of the active site with the large QM regions typically 100 200 atoms in appli cations we have pursued that are in many cases necessary t
72. rom the QSite panel but larger systems must be run them from the command line See Section 4 10 on page 43 for more information Cartesian constraints may be placed on atoms in both the QM and the MM regions See Section 4 4 on page 31 for a description of the two types of constraints Frozen atom constraints can be applied to atoms in both regions Constrained atoms can be specified for MM region atoms but are ignored if applied to QM region atoms In general a QSite calculation can only be performed using a single entry If you want to run a QSite job using the Workspace structure as input and that structure includes multiple entries combine them into a single entry using the Merge option from the Entry menu in the Project Table panel The merged entry should be the only entry included in the Workspace when you start the job One exception to this is when setting up a transition state search In this case you may select up to three Project Table entries depending upon the algorithm that is selected for performing the search See Section 4 7 for more information about transition state searching 4 1 The QSite Panel QSite calculations can be set up and run using the QSite panel To open the QSite panel choose QSite from the Applications menu At the top of the panel is an option menu for selecting the source of structure input which is described in the next subsection The center section of the panel has six tabs QSite 5 0 User Manual
73. run a job the syntax is SSCHRODINGI ER qsite run options jobname in The in suffix for the input file jobname in is optional if it is not specified it is added The options for running Table 5 2 Options Option QSite calculations are described in Table 5 2 for running QSite jobs Description PROCS nprocs SAVI eai WAIT Run the job using nprocs processors A parallel Jaguar license is required for this option Do not specify multiple processors if continuum solvation is in use Save the scratch directory do not delete it at the end of the job Wait for the job to finish before executing the next command If the job is run from a terminal window the prompt is not displayed until the job finishes This is useful in command scripts in which you have specified actions to take only after the QSite job finishes QSite 5 0 User Manual Chapter 5 Running QSite from the Command Line The gsite command accepts the standard Job Control options which are given in Section 4 3 of the Job Control Guide You can use the QSite job to query Job Control for information about hosts and software versions The syntax of the query command is SCHRODINGER gsite information option The information options are given in Section 4 3 of the Job Control Guide The qsite command also has its own commands for querying Job Control about jobs controlling jobs and obtaining some other information The syntax
74. sasssssssosssneoss 23 50 specifying calculation 37 Jobs EE unse 43 QSite 5 0 User Manual 67 Index 68 K keywords adding Jaguar from GUI 23 MM minimization mmkey section potential energy qmregion Section QSite gen section L ligands adding to the QM region 26 covalently bound 26 Linear Synchronous Transit LST method 38 long range forces in TN optimizations 37 M Maestro starting s ssssmssssssrsrssrsrsrsrerrsrernerrsrsrrn rr rna 2 merging project entries for QSite 19 metals adding to the QM region 26 adjusting charges seesseseeseerseerserssesrses 14 covalent bonds to protein 14 possible problems with 44 MM Constraints tab 32 MM Minimization tab 36 MM region er Ee sn si 21 interaction with QM region 01 leaving backbone in a25 molecular orbital surfaces 40 multimeric protein structures s ssesseeseeeee 14 N net charge QM region sssesssssseseserserersesereees 23 non bonded cutoffs 29 O OUtput files een overview of protein preparation P parallel processing seseeeeeeseeeerereerersererereeeee 1 KESIC ONS u a 30 QSite 5 0 User Manual parameterization frozen orbital cuts basis set USE 080er 28 force field used nn 2
75. ssion of jobs to Schr dinger s computational programs The main Maestro features include a project based data management facility a scripting language for automating large or repetitive tasks a wide range of useful display options a comprehensive molecular builder and surfacing and entry plotting facilities For detailed information about the Maestro interface see the Maestro online help or the Maestro User Manual Protein Preparation for use in QSite can be performed for most protein and protein ligand complex PDB structures using the Protein Preparation Wizard panel in Maestro 1 2 Running Schrodinger Software To run any Schr dinger program on a UNIX platform or start a Schr dinger job on a remote host from a UNIX platform you must first set the SCHRODINGER environment variable to the installation directory for your Schr dinger software To set this variable enter the following command at a shell prompt QSite 5 0 User Manual Chapter 1 Introduction csh tcsh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory Once you have set the SCHRODINGER environment variable you can start Maestro with the following command SSCHRODINGER maestro amp It is usually a good idea to change to the desired working directory before starting Maestro This directory then becomes Maestro s working directory For more information on starting Maestro see Section 2 1 of the Maestr
76. st extend at least as far as the first permissible cut between pro tein atoms e Specifying cuts between atoms for which the QM region will be capped with hydrogen atoms Hydrogen caps can be placed on any atom designated to be in the QM region provided that it is singly bonded to an atom in the MM region and that any two such MM atoms are separated in the MM region by at least three bonds This option offers much more flexibility in the selection of the QM region The MM atom is replaced with a hydrogen atom in the QM calculation which leaves a chemically well defined structure with no dangling bonds The QM Settings tab features are described below BAE QM settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces Scan Method DFT B3LYP 1 Spin unrestricted Charge 0 Multiplicity 1 QM options iacc 1 vshift 1 0 maxit 100 mi a Hydrogen cap electrostatics Gaussian charges 1 F Pick Hydrogen cap W Show markers Delete entire residue entire residue entire residue ligand ion hydrogen cap VAL 212 2 OM atom 1267 MM atom 1270 Delete All Update QM Region Display Total number of atoms in QM region 31 Start Read Write Close Help Figure 4 1 The QM Settings tab of the QSite panel showing the QM Region subtab QSite 5 0 User Manual Chapter 4 Running
77. st frequency eigenvector of the Hessian and to minimize along all other modes Again only the QM and interfacial MM atoms are included in the deter mination of the Hessian as all pure MM atoms are adiabatically minimized at each TS search step 6 3 How QSite Works Most approaches for developing robust and accurate QM MM methods have been based on link atom approaches in which QM and MM fragments are capped by hydrogens These methods face nontrivial problems in constructing an accurate description of the QM MM inter face particularly for polar systems where the treatment of electrostatic interactions can be highly problematic While progress has been made we do not believe that a fully satisfactory link atom methodology is available QSite takes an alternative approach in which frozen local ized molecular orbitals are used to build the QM MM interface This methodology has recently been reviewed favorably 3 As far as we are aware QSite is the first ab initio frozen orbital methodology with analytical gradients for which accuracy for structures and conformational energetics of a polar system has been demonstrated The details of QSite s frozen orbital interface technology is provided in References 4 6 at the end of this chapter The key aspects are e The frozen orbital itself is obtained by Boys localization of the quantum chemical wave function for one of a series of small template molecules The orbital must be translated and
78. structures needed for a QSite job are in the associated Maestro file Instead the input file contains a MAEFILE pointer to a valid Maestro structure file QSite 5 0 User Manual 49 Chapter 5 Running QSite from the Command Line 50 In addition to the Jaguar sections there are two sections qmregion and mmkey for defining the QM region and for setting parameters for the MM part of the calculation These sections are described below As in the Jaguar keyword tables the value given in bold italics is the default value 5 3 1 Additions to the gen Section In addition to the Jaguar keywords there are some QSite specific keywords that can be added to the gen section These keywords are described in Table 5 4 Table 5 4 Additional gen section keywords Keyword Value Description hcapeschg 0 Ignore electrostatic interactions between the QM and MM regions entirely in the vicinity of ahydrogen cap Van der Waals interac tions are still included 1 Use modified point charges to represent the potential of the atoms near the cap and MM point charges for the rest of the MM region 2 Use Gaussian charge distributions to represent the potential of the atoms near the cap and MM point charges for the rest of the MM region impversion medium Use the default impact version 8000 atoms bonds Default huge Use the large impact version 40 000 atoms bonds mmqm 0 Do not run QSite This is the default 1 Run QSite This setting must
79. t This is a good general optimization method and is the default method e Steepest descent This can be a good method for initiating a minimization on a starting geometry that contains large steric clashes Convergence is very poor towards the end of minimization where the conjugate gradient algorithm should be used Initial step size Specifies the initial step size of the minimization cycle for conjugate gradient and steepest descent minimizations in this text box The default value is 0 05 but any positive value is allowed Maximum step size Specify the maximum step size of the minimization cycle for conjugate gradient and steepest descent minimizations in this text box If the step size exceeds this value the minimization will halt The default value is 1 00 A but any positive value is allowed The maximum step size is the maximum displacement allowed for an atom in any step of a minimization calculation QSite 5 0 User Manual 35 Chapter 4 Running QSite From Maestro 36 QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization surfaces scan Minimization options for the MM region Maximum cycles 1000 Algorithm Conjugate gradient Initial step size 0 05 Maximum step size 1 000 Convergence criterion Energy and gradient Energy change criterion 0 1 Gradient criterion 0 01 Start Read Write Close Help Figure 4
80. tain waters cofactors and metal ions and can also be multimeric The structure generally has no information on bonding or charges Terminal amide groups can also be misaligned because the X ray structure anal ysis cannot usually distinguish between O and NH For QSite calculations which use an all atom force field atom types and bond orders must be assigned the charge and protonation states must be corrected side chains reoriented if necessary and steric clashes relieved This section provides an overview of the protein preparation process The entire procedure can be performed in the Protein Preparation Wizard panel which you open from the Workflows menu on the main toolbar This tool and its use is described in detail in Chapter 2 of the Protein Preparation Guide After processing you will have files containing refined hydrogenated structures of the ligand and the ligand receptor complex The prepared structures are suitable for use with QSite In most cases not all of the steps outlined need to be performed See the descriptions of each step to determine whether it is required QSite 5 0 User Manual Chapter 3 Protein Preparation 14 You may on occasion want to perform some of these steps manually Detailed procedures are described in Chapter 3 of the Protein Preparation Guide 1 Import a ligand protein cocrystallized structure typically from PDB into Maestro The preparation component of the protein preparation f
81. ther third party software or linked sites do not constitute an endorsement by Schr dinger LLC Use of such other third party software and linked sites may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for such other third party software and linked sites or for damage resulting from the use thereof Any warranties that we make regarding Schr dinger products and services do not apply to such other third party software or linked sites or to the interaction between or interoperability of Schr dinger products and services and such other third party software September 2008 Contents Document CONVENtiONS ae vii Chapter intense aie 1 Ti About e E 1 1 2 Running Schrodinger Software 1 1 3 Citing QSite in Publications ossssessrsrsrsrsrsssssrsrsssrsrrssrs eran arenan ana a arenan aan sanera nn 2 Chapter 2 EN ET EE 3 2 1 Preparing a Working Directory AA 3 2 2 Starting RE EE 3 2 3 Importing the Complex 4 2 4 Setting Up the Display Elend 4 2 5 Selecting the QSite Job Type 5 2 6 Defining a QM Region 6 2 7 Running the QSite Job RK 7 2 8 Examining Results tarn A S 8 2 8 1 Comparing Input and Output Structures sisside apinn n r rs 9 2 8 2 Comparing Ligand Receptor Interactions sisisms sssssisivssssinsssinsie aaie 9 Chapter 3 Protein P BaRiiOn esse 13 3 1 Protein Preparation Procedure 13 3 2
82. tic potential Box size adjustment 0 00 Ayside ESP units kcal mol z Grid density 5 00 pech 1 Electron density Spin density M Molecular orbitals Alpha From HOMO 2 0 to LUMO 0 Total number of orbitals 2 Beta From HOMO ln te LUMO ln Total number of orbitals 2 Start Read Write Close Help Figure 4 9 The Surfaces tab Molecular orbitals Calculate the specified molecular orbitals on the grid Not available for MP2 calculations To specify the desired orbitals choose the references for the molecular orbital indices from the From and to option menus and enter the relative index in the text box The option menu choices are e HOMO Count down from the HOMO inclusive e LUMO Count up from the LUMO inclusive Thus From HOMO 0 to LUMO 0 includes both the HOMO and the LUMO The controls for beta orbitals are only available for UHF and UDFT wave functions Box size adjustment Enter a value to adjust the size of the box used to calculate the grid The default box size encompasses the van der Waals radii of all atoms in the molecule 5 Sets iorbla iorb2a iorb1b iorb2b in the gen section 6 Sets xadj yadj zadj in the gen section QSite 5 0 User Manual Chapter 4 Running QSite From Maestro Grid density Enter the number of grid points per angstrom 4 9 The Scan Tab In this tab you set up the coordinates for a relaxed or a rigid coord
83. tion also contains a Show markers option which is selected by default Atoms to be frozen are marked with ared cross and a padlock icon in the Workspace Atoms to be constrained are marked with a brown cross and a spring icon in the Workspace display QSite 5 0 User Manual Chapter 4 Running QSite From Maestro Constrained Atoms Constraining force 25 00 Define constrained atoms F Pick Residues All Selection Previous Select W Show markers Delete Delete All Close Help Figure 4 5 The Constrained Atoms panel To distinguish the currently selected frozen or constrained atom Maestro colors the marker turquoise Constraining force The Constraining force text box sets the value of the harmonic force constant applied to the selected constrained atoms The same force constant is used for all atoms The default is 25 00 kcal mol A Deletion buttons The constraint on the currently selected atom can be removed by clicking Delete The atom is then removed from the atoms list To remove all constraints of this type click Delete All The atoms list is then cleared 4 5 The QM Constraints Tab The QM constraints tab is used to set constraints on geometric parameters in the QM region It provides the same capabilities as in the Optimization tab of the Jaguar panel For full details see Section 4 2 of the Jaguar User Manual Briefly you can set constraints on distanc
84. to remain near their initial coordinates by applying a harmonic force Atom constraints in QSite for atoms in the MM region must be set in the MM Constraints tab The Constraints tab contains two buttons Frozen Atoms e Constrained Atoms QSite 5 0 User Manual 31 Chapter 4 Running QSite From Maestro 32 QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization Surfaces scan Frozen Atoms Constrained Atoms Start Read Write Close Help Figure 4 4 The MM Constraints tab of the QSite panel These buttons open the Frozen Atoms and Constrained Atoms panels These panels have a similar structure The panel features are described below Atoms list The upper portion of each panel is a text area that lists the atom number of each atom that has been selected to be frozen or constrained The currently selected atom is highlighted Picking tools This section labeled Define Frozen Atoms or Define Constrained Atoms contains standard picking controls a Pick check box and menu which is set to Atoms by default an All button a Select button which opens the Atom Selection dialog box If you deselect the Pick check box you can use the Workspace selection tool to select atoms then click the Selection button to add those atoms to the list or use the Previous button to return to the most recent selection The picking tools sec
85. traint section next to the table and enter the value that you want the constraint to converge on in the Target value text box This value is copied to the Target column of the table To delete one or more constraints select them in the table and click Delete in the Selected constraint section To delete all constraints click Delete All QSite 5 0 User Manual Chapter 4 Running QSite From Maestro 4 6 The MM Minimization Tab The MM Minimization tab specifies settings for Impact energy minimization of the MM region of the molecule If the QM method chosen in the Optimization tab is Single point these settings are not used and no MM minimization is performed The options available in this tab are described below Maximum cycles Set the maximum number of cycles for the minimization calculation in this text box The mini mization terminates if it has not converged by this point The default value of this setting is 100 iterations but you can specify any value greater than or equal to zero Zero cycles is a special case it instructs Impact just to evaluate the energy for the current coordinates Algorithm Choose the minimization algorithm from this option menu The choices are e Truncated Newton TN This is a very efficient method for producing optimized struc tures A short conjugate gradient pre minimization stage is performed first to help improve the convergence of the Truncated Newton algorithm e Conjugate gradien
86. typing in the entry name from the Project Table by clicking Choose and selecting the entry from a list or if the structure is in the Workspace by selecting Pick to define entry and clicking on any atom in the structure 4 8 The Surfaces Tab In this tab you can set options to generate electrostatic potential electron density spin density and molecular orbital surfaces at the end of the QSite job When you request molecular orbital surfaces any frozen orbitals from frozen orbital cuts are ignored If for example you request a surface for the HOMO the surface is generated for the highest energy occupied orbital that is not frozen The options available in this tab are described below Electrostatic potential Calculate the electrostatic potential ESP on the grid The units used to represent the ESP can be selected from the ESP units option menu Electron density Calculate the electron density on the grid Spin density Calculate the electron spin density on the grid sets iplotden 1 in the gen section Only available for UHF and UDFT wave functions Sets iplotesp 1 in the gen section Sets espunit in the gen section Sets iplotden 1 in the gen section Sets iplotspn 1 in the gen section DT QSite 5 0 User Manual 39 Chapter 4 Running QSite From Maestro 40 QM Settings Potential MM Constraints OM Constraints MM Minimization OM Optimization Surfaces scan W Electrosta
87. uar s ability to handle large systems efficiently and to accelerate the SCF convergence yields a methodology of unprecedented power and flexibility No other commercially available program can provide the kind of chemical insight and quantitative description for metal containing enzymes that QSite offers As described below QSite also allows reactive processes to be modeled and transition states to be located For applications such as these QSite is an essential part of a comprehensive computational strategy for struc ture based drug design 6 2 QM MM Transition State Modeling Jaguar and QSite can perform transition state TS searches by using a quasi Newton method to find the TS nearest the initial geometry 1 Alternatively Jaguar can employ a Linear Quadratic Synchronous Transit LST QST approach which is also known as Synchronous Transit Quasi Newton STQN to guide the search along the reaction pathway between speci fied reactant and product geometries 2 This latter approach is clearly superior and has now been extended for use in QSite Through the Maestro GUI you can enter one of the following 1 Initial guess for the TS a simple TS search is then used 2 Reactant product and TS guess QST is used with the entered guess used as the initial TS geometry 3 Reactant and product geometries LST is used but an initial TS geometry is generated automatically For case 3 the automatic generation is done by interpolating
88. ucture the structure in the Workspace for the transition state It attempts to find the saddle point closest to the starting structure by maximizing the energy along the lowest frequency mode of the Hessian and minimizing the energy along all other modes e LST Linear Synchronous Transit is useful if you have initial guess structures for the reac tant and the product and want QSite to look for a transition state structure by interpolat ing between them LST uses a quasi Newton method to search for the optimum transition state geometry choosing a transition state guess structure based on the interpo lation value you set using the Fraction of path between reactant and product slider By QSite 5 0 User Manual Chapter 4 Running QSite From Maestro default it is set at 0 50 directing QSite to choose an interpolated transition state guess structure midway between the reactant and the product If you want to pick a guess struc ture closer to the reactant move this slider toward 0 00 For a guess structure closer to the product move the slider toward 1 00 e QST Quadratic Synchronous Transit is useful if you have initial guess structures for the reactant the product and the transition state QST uses a quasi Newton method to opti mize the transition state geometry The structures that define the transition state initial guess can be specified in the Reactant entry Product entry and TS guess entry sections You can select the entry by

QSite User Manual - The Friesner Group

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