QSite Panel

Rules and Procedures for Creating the QM/MM Boundary

There are three general ways to define the QM/MM boundary for QSite. Two methods set the boundary across a covalent bond. In the frozen orbital method, the boundary must be placed across a bond to an alpha carbon in an amino acid residue. Special parameters are used to properly describe the energetics associated with motion of the atoms at the QM/MM interface. The link-atom method, also called the hydrogen-cap method, can be used with any single bond, regardless of the elements at the ends of the bond. The bond in this method is capped with a hydrogen atom, which leaves a chemically well-defined structure with no dangling bonds. The third method can be used only for free (i.e., not covalently bound to anything) molecules or ions. In this method the entire molecule or ion is placed in the QM region, and the QM/MM "boundary" is simply in the space between the free molecule and the rest of the structure.

A more detailed discussion of each type of boundary definition follows.

Side Chain Cuts (frozen-orbital method)

To place the QM/MM boundary between an amino acid side chain and the protein backbone, choose Side chain from the Pick option menu and click on any atom in the residue. The side chain for that residue will be placed in the QM region.

Side chain cuts are not possible in PRO, and are not permitted in GLY or ALA because the side chains are so small. Side chain cuts are also not permitted if the side chain has been modified within 3 atoms of the alpha carbon atom.

Backbone Cuts (frozen-orbital method)

In order to define a cut along the protein backbone, choose Entire residue from the Pick option menu. You must now click on two atoms to define the range of residues to be placed into the QM region. All residues in between the two selected atoms will treated as part of the QM region.

Backbone cuts are placed in a bond to an alpha carbon that is in an amino acid residue, but you may click on any atom in a residue to define a backbone cut. The rule is that the cut will be placed so as to ensure that the atom you select ends up in the QM region. After you have selected two atoms, Maestro highlights the QM region so that you can see how big it is and where the QM/MM boundary cuts are located.

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 region.

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.

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 carbonyl group and an extra N-H bond from the neighboring residues.

Free Ligand/Ion

In order to place an entire molecule or ion into the QM region, choose Free ligand/ion from the Pick option menu. There are no restrictions on this selection method. Starting from the atom that you pick, the atomic connectivity (if any) is followed outward until it terminates, and all atoms found along the way are considered to be part of that molecule and are placed in the QM region.

Hydrogen Caps (link-atom method)

To cap covalent single bonds with a hydrogen atom, choose Hydrogen cap from the Pick option menu. You must now click on two atoms. The first atom is placed in the QM region. The second atom is replaced with a hydrogen atom (but generally at a closer distance to the QM atom since bonds to hydrogen are shorter than bonds to other elements). Once you have capped all desired bonds, click Update QM Region Display. Maestro highlights all atoms connected directly or indirectly to the hydrogen caps, and places these into the QM region. If Maestro highlights many more atoms than you expect, it probably means that you omitted a hydrogen cap somewhere such that your QM region is still covalently bound to the rest of the system.

The MM sides of two hydrogen caps must have at least three bonds between them in the MM region. That is, the MM atoms replaced by hydrogens must be at least three bonds apart if all atoms between them are MM atoms. There are no such restrictions on the QM sides for hydrogen caps.

Recommendations and Limitations

• The hydrogen-cap method is quite general, and not limited to protein-ligand complexes. You can use it on any large molecular system, subject to the limitations of atom types and force field parameters for the atoms that you place in the MM region. There are a few atom types for metals, but in many cases metals and their attached ligands will have to be included in the QM region. This is the default and recommended method.

• If you are working with proteins, and if you want to place in the QM region a residue whose side chain has been modified, such as by covalently attaching a ligand or some other chemical functionality, then you might not be able to make side chain cuts (see the above discussion of side chain cuts). You can make backbone cuts so as to place the entire modified residue in the QM region, or you can use hydrogen caps.

• To include disulfide bridges or other bridging species in the QM region, you can either use backbone cuts or hydrogen caps.

QSite Panel Features

• QM Settings tab
• Potential tab
• MM Constraints tab
• QM Constraints tab
• MM Minimization tab
• QM Optimization tab
• Properties tab
• Scan tab
• Job toolbar
• Status bar

• QM Settings
• Potential
• MM Constraints
• QM Constraints
• MM Minimization
• QM Optimization
• Properties
• Scan

QM Settings Tab Features

Use this tab to enter information for the quantum mechanics (QM) calculation, and to define the region to be treated quantum-mechanically.

The QM information includes the QM method to be used, the charge and spin multiplicity of the QM system, and other keywords and options that may be required by Jaguar. For more information on Jaguar options, see the Jaguar User Manual.

The QM region is defined using any of the following methods:

• Specifying hydrogen caps on atoms that are in the QM region that are singly-bonded to atoms in the MM region.
• Selecting the ligand, metal ions, or other disconnected species that are not covalently bonded to the protein.
• Specifying cuts between certain covalently-bonded atoms in connected peptide residues.

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. Any two such MM atoms must be 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.

QSite cuts are specially parametrized 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).

Cuts in a protein-ligand complex must be between atoms in peptide residues. Covalently-bound ligands can be included in the QM region when defining cuts, but only along with attached protein atoms. The QM region must extend at least as far as the first permissible cut between protein atoms.

Waters that interact with the ligand or influence the protein near the ligand should be added to the QM region. Other waters can be added to the MM region.

If you have a metal in the structure it should either be added to the QM region, or it should be frozen in the MM region along with its ligands or ligand residues.

See Rules and Procedures for Creating the QM/MM Boundary for more detail.

The QM Settings tab contains a set of general controls, and two subtabs.

• General Settings
  • Method option menu
  • Spin-unrestricted option
  • Charge text box
  • Multiplicity text box
  • QM options text box
  • Hydrogen cap electrostatics option menu
  • Use wave function in input file option
  • Use Hessian in input file option
• QM Region subtab
  • QM region table
  • Pick option and menu
  • Show markers option
  • Delete and Delete All buttons
• QM Basis subtab
  • Basis set table
  • Pick option and menu
  • Show markers option
  • Basis set option menu

General Settings

The general settings at the top of the panel define the type of QM calculation to perform.

Method option menu

The options for the QM method include several density functional theory methods (DFT: B3LYP, DFT: PWB6K, DFT: M06, DFT: M06-2X, DFT: M06-L, DFT: M06-HF, DFT: M05, DFT: M05-2X), Hartree-Fock (Hartree-Fock) and local Møller-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. Several dispersion corrected DFT methods are also available (DFT: B3LYP-D3, DFT: M06-2X-D3, DFT: B3LYP-D3(BJ), DFT: wB97X-D, DFT: B97-D3). To use another dispersion corrected DFT method, you can setdftname=functional-d3 in the QM options text box.

For more information on QM methods, see the Jaguar User Manual — Contents. Details of the DFT methods are available in Density Functional Theory.

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 text box

This is the net charge of the QM region of the system. Maestro updates the Charge to a reasonable 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 text box

This text box displays the 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 calculation halts with an error message. The charge and multiplicity of the QM region must be consistent.

QM options text box

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 blanks. 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 The Jaguar Input File for more information on Jaguar keywords.

Note: TDDFT is not supported with QSite, so you cannot add an itddft setting in this text box.

Hydrogen cap electrostatics option menu

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.

• Gaussian grid—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, with the Gaussian charge distribution and potential represented on a grid.
• Gaussian charges—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. The potential is calculated analytically, but is not available for excited state calculations, or for properties that require a CPHF calculation. Use Gaussian grid instead.
• 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.
• None—Ignore electrostatic interactions between the QM and MM regions in the region of the caps. Van der Waals interactions are still included.

Use wave function in input file option

Use Hessian in input file option

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.

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:

• hydrogen cap—QM atom=number, MM atom=number
• side chain—Residue name and number
• entire residue—Residue name and number
• ligand/ion—Molecule 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.

Pick option and menu

Select this 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 molecule, or an ion.

Hydrogen cap

To define cuts that are capped by hydrogen atoms (rather than atoms with frozen orbitals), choose 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 Hydrogen cap electrostatics option menu in the general section becomes available, and you can choose the electrostatic treatment of MM atoms near the cap.

This is the default and recommended method.

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 with ball and stick markers in sienna if Show markers is selected. A cut is made between the alpha carbon and beta carbon of that residue. All of the atoms in the side chain are included in the QM region.

Side-chain cuts can be made in any peptide residue other than alanine (ALA), glycine (GLY), and proline (PRO). (To incorporate these side chains in the QM region, you must use backbone cuts and include the entire residue.) 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.

The force field for the MM region must be OPLS_2005, as the cuts are parametrized for this force field.

Entire residue

To add entire amino acid residues to the QM region, choose this option and then pick two backbone 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 marked 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). An exception is that backbone cuts on PRO residues cannot be made between the N atom and the Cα 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 carbonyl group and an extra N-H bond from the neighboring residues.

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 region.

The cuts made with this choice use the frozen-orbitals method for defining the terminus of the QM region.

The force field for the MM region must be OPLS_2005, as the cuts are parametrized for this force field.

Free ligand/ion

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. Choose 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.

Note: If the structure contains a metal atom, it should be either included in the QM region or it should be frozen, if it is in the MM region, along with its ligands or ligand residues.

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.

Delete and Delete All buttons

To remove atoms from the QM region or redefine cuts, select the rows in the QM region table and click Delete. Take care to ensure that the resulting QM region is consistent with any backbone cuts that have been made.

To clear the QM region definition, click Delete All.

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 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.

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 parametrization of the frozen orbital cuts.

Potential Tab Features

The Potential tab contains options for the definition of the potential energy functions used in the molecular mechanics part of a QSite calculation.

• Force field option menu
• Electrostatic treatment option menu
• Dielectric constant text box
• Use non-bonded cutoffs option and Settings button
• Use atomic partial charges in structure file option
• Skip force field checks option

Force field option menu

Select the molecular-mechanics force field to use for the calculation, from OPLS_2005 and OPLS4. The default is OPLS_2005, and this force field is the only one available for protein cuts.

Electrostatic treatment option menu

This option menu offers two methods for calculating the electrostatic component of the molecular mechanics energy:

Constant dielectric

This option calculates the electrostatic interaction between atoms i and j as:

E_ele = 332.063762 q_iq_j / (εr_ij)

A constant dielectric is appropriate for a vacuum (gas-phase) calculation or when an explicit solvent model is used.

Distance dependent

This option calculates electrostatic interaction between atoms i and j as:

E_ele = 332.063762 q_iq_j / (εr_ij²)

A distance-dependent dielectric is sometimes used as a primitive model for the effects of solvent. In this model, the electrostatic interaction between a pair of atoms falls off rapidly as the distance between the atoms increases. Explicit solvent models are much better at accounting for solvent effects than a distance-dependent dielectric.

The variables in the above formulae are defined as follows:

• E_ele is the electrostatic interaction in kcal/mol
• q_i and q_j are the partial atomic charges on atom i and j
• r_ij is the distance in Å between atoms i and j
• ε is the Dielectric constant (see below)

Dielectric constant text box

Use this text box to specify the dielectric constant ε used in the electrostatic calculations. The default is 1.0.

Use non-bonded cutoffs option and Settings button

This option is selected by default. Click Settings to open the Truncation Panel.

In molecular-mechanics calculations it is often impractical to include the nonbonded (electrostatic and van der Waals) interactions between every pair of atoms. For large systems, many such pairs are separated by a great distance and contribute little to the interaction energy. Judicious 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.

Use atomic partial charges in structure file option

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 not be used for a system in which you make frozen orbital cuts, as the resulting structure and properties will generally be erroneous. The handling of frozen orbitals involves a parametrization 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.

Note also that 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 molecular charge.

Skip force field checks option

Bypass force-field checks during atom typing. 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. Selecting this option can avert failure for metal atoms.

MM Constraints Tab Features

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 to remain near their initial coordinates by applying a harmonic force. In QSite, atoms in both the QM and the MM regions can be frozen or constrained. In this tab you specify the MM atoms to be frozen or constrained. Use the QM Constraints tab to specify QM constraints.

Frozen Atoms button

Click this button to open the QSite — Frozen Atoms Panel, in which you can select the atoms to be treated as frozen. Both QM-region and MM-region atoms can be frozen.

Constrained Atoms button

Click this button to open the Constrained Atoms Panel, in which you can select the MM-region atoms to be constrained.

QM Constraints Tab Features

Set constraints on geometric parameters in the QM region. Specified atoms can be frozen at their input coordinates, or they can be constrained to remain near their initial coordinates by applying a harmonic force. In QSite, atoms in both the QM and the MM regions can be frozen or constrained. In this tab you specify the QM atoms to be frozen or constrained. Use the MM Constraints tab to specify MM constraints.

This tab provides the same capabilities as in the Optimization tab of the Jaguar panel. Briefly, you can set constraints on distances, 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 individual 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.

For full details, see Constraining Coordinates in Jaguar Calculations.

The terminology for constraints differs a little from that used for MM constraints. Here, a constraint is a frozen atom or internal coordinate, and a dynamic constraint is a constraint in which a harmonic potential is applied.

• Add New Constraint section
  • Type option menu
  • Pick option menu
  • Dihedral button
• Constraints table
• Selected constraint section
  • Dynamic option
  • Value text box
  • Delete and Delete All buttons

Add New Constraint Section

Choose a constraint type and pick atoms in the Workspace to define the constraint. You can pick atoms in the MM region to enforce constraints across the boundary, provided that at least one atom is in the QM region. When you have picked the required number of atoms for the constraint type, the constraint is listed in the Constraints table. Cartesian constraints are marked with an asterisk in the zmat section; distance, angle, and dihedral constraints are added to the coord section, which is created if it does not exist.

Type option menu

Choose the type of constraint. Choices are Angle, Cartesian, Distance, and Dihedral. If you choose Cartesian, the Constrain in option menu becomes available.

Pick option menu

Choose an object to pick from this option menu, then pick atoms in the Workspace to define the constraint. When you choose from this menu, the Pick option is automatically selected. The available objects are Atom for Cartesian constraints, and Atom and Bond for all other types of constraint. The atoms are marked in the Workspace as you pick them, and each constraint is marked in the Workspace and entered in the Constraints table as it is completed.

Dihedral button

Open the Dihedral Selection panel to select standard protein dihedral angles. This button is only available when you choose Dihedral from the Type option menu and select Pick.

Constraints Table

Displays the constraints with their type, and also the target value, if it is a dynamic constraint. You can select one row at at time in the table. The constraint for the selected row is highlighted in the Workspace, and you can edit the constraint or delete it in the Selected Constraint section.

Selected Constraint Section

In this section you can edit or delete the constraint selected in the Constraints table.

Dynamic option

Make the constraint dynamic. You must also set a target value in the Value text box.

Value text box

Set a target value for the dynamic constraint. This is the value that the constrained coordinate should have when the optimization is complete.

Delete and Delete All buttons

Delete the selected constraint or all constraints.

MM Minimization Tab Features

Specify settings for energy minimization of the MM region of the system. If the QM method chosen in the QM Optimization tab is Single point, these settings are not used, and no MM minimization is performed.

• Maximum cycles text box
• Algorithm option menu
• Initial step size text box
• Maximum step size text box
• Convergence criteria option menu
• Energy change criteria text box
• Gradient criteria text box
• Update long range forces every N steps
• Long range force cutoff > d Å

Maximum cycles text box

Use this text box to set the maximum number of cycles for the minimization calculation. The minimization ends 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. A value of 0 is a special case which specifies a single-point energy calculation at the current coordinates.

Algorithm option menu

This option menu is used to select the minimization algorithm. The choices are:

• Truncated Newton— This is a very efficient method for producing optimized structures. A short conjugate gradient preminimization stage is performed first to help improve the convergence of the Truncated Newton algorithm. However, it is sensitive to small differences in the input structure, and does not always find the same minimum.

• Conjugate gradient— This is a good, general, and stable optimization method, and is the default method.

• 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 method should be used.

Initial step size text box

For conjugate gradient and steepest descent minimizations, specify the initial step size of the minimization cycle. The default initial step size is 0.05 Å, but any positive value is allowed.

Maximum step size text box

For conjugate gradient and steepest descent minimizations, specify the maximum step size of the minimization cycle. If the step size exceeds this value the minimization stops. The default value is 1.000 Å, but any positive value is allowed. The maximum step size is the maximum displacement of an atom in any step of a minimization calculation.

Convergence criteria option menu

Use this option menu to determine whether the minimization must satisfy an energy change criterion, a gradient criterion, or both, to be considered converged. The values for these criteria are set below. The options are:

• Energy and gradient (the default)
• Energy
• Gradient

Energy change criterion text box

Specify the energy change criterion for convergence. The default is 0.1 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 text box

Specify the gradient criterion for convergence. The default is 0.01 kcal/(mol Å), but any positive value is allowed. The criterion is satisfied if the norms of two successive gradients differ by less than the specified value.

Update long range forces every n steps text box

Specify the frequency with which long range forces are updated for truncated Newton minimization. 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 convergence, 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 > d Å text box

Specify the distance beyond which forces are considered long range and are therefore updated every n steps, for truncated Newton minimization. The default value is 10.000 Å.

QM Optimization Tab Features

The QM Optimization tab specifies the QM (Jaguar) calculation to be performed and provides information needed to set up the calculation. This includes specifying additional structures that may be needed for transition state optimizations (reactant, product, and transition state guess structures). Optimizations (both minimizations and transition state optimizations) are performed using redundant internal coordinates.

• Method option menu
• Maximum number of iterations text box
• Save all structures in output Maestro file option
• TS method option menu
• Reactant entry specification options
• Product entry specification options
• TS guess entry specification options
• Fraction of path between reactant and product slider

Method option menu

This option menu controls the QSite calculation type:

• 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. You can continue setting up your single-point calculation in the QM Settings tab.

• Minimization—Locate a minimum-energy structure by geometry optimization. By default both the MM region and the QM region are optimized. If you want to optimize only the QM region, set the number of minimization steps to 0 in the MM Minimization tab. There is no need to explicitly freeze the MM-region atoms.

• Transition state—Locate a transition state structure by geometry optimization.

Maximum number of iterations text box

If you have chosen a minimization or transition state calculation, set the number of optimization iterations. The default value is 100 iterations.

Save all structures in output Maestro file option

Save all intermediate structures to the Maestro output file. This option can create large files, because it includes the QM and MM regions. Sets ip472=2 in the gen section.

TS Method option menu

If you have chosen a transition state calculation, select one of three types of transition state optimization that are supported in QSite, corresponding to well-known ab initio techniques:

• Standard—Use the standard TS optimization method. Search for the saddle point closest to the starting structure by maximizing the energy along the lowest-frequency mode of the Hessian, and minimize the energy along all other modes. Useful if you only have a single initial guess structure (in the Workspace) for the transition state.

• LST—Use the Linear Synchronous Transit method. Given reactant and product structures, along with an interpolation value between them set with the Fraction of path between reactant and product slider, use a quasi-Newton method to search for the optimum transition state geometry.

• QST—Use the Quadratic Synchronous Transit method. Given reactant, product, and transition state guess structures, use a quasi-Newton method to optimize the transition state geometry.

See Transition-State Optimizations and Transition-State Search Suggestions for detailed information about these methods.

Reactant entry specification options

In the text box, type the name of the entry you want to represent the reactant structure; click the Choose button and select it from the list; or use the Pick to define entry option to select it in the Workspace. The selected entry name will then appear in the text box. The entry must be one of the entries in the current project's Project Table.

Product entry specification options

In the text box, type the name of the entry you want to represent the product structure; click the Choose button and select it from the list; or use the Pick to define entry option to select it in the Workspace.

TS guess entry specification options

In the text box, type the name of the entry you want to use as a guess for the transition state structure; click the Choose button and select it from the list; or use the Pick to define entry option to select it in the Workspace.

Fraction of path between reactant and product slider

Available when an LST transition state search has been selected. The default setting is 0.50, directing QSite to choose an interpolated transition state guess structure midway between the reactant and the product. If you wish to pick a guess structure closer to the reactant, move this slider to a value between 0.00 and 0.50. For a guess structure closer to the product, select a value between 0.50 and 1.00.

For more information about QM calculations and transition state search methods, see the Jaguar User Manual.

Properties Tab Features

In this tab, you select the properties you want to calculate and set any relevant options. Before you can do so, you must specify the QM region in the QM Settings tab.

The tab consists of a table listing all the available properties, and controls for each of the properties that are displayed in the lower portion of the tab when you select the row for the property in the table.

As in Jaguar, the list of available properties depends on the method selected.

In addition to restrictions on the properties due to the method, there are also restrictions that are based on the nature of the QM/MM boundary. Properties that are not available due to the definition of the QM region are dimmed in the Properties table of the tab. Specifically, frequencies, NMR shielding constants, and polarizabilities are not available if there are frozen-orbital cuts. Also, the Pulay SQM scaling of frequencies is not available at all.

Properties are calculated from the QM orbitals, but frozen orbitals from frozen-orbital cuts are ignored. For example, if you request a surface for the HOMO, the surface is generated for the highest-energy occupied orbital that is not frozen. The QM orbitals include effects from the MM region, but the MM region is not explicitly included in any of the properties.

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 representation of the wave function near the cuts does not accurately represent the wave function of the full system.

• Properties table
• Vibrational frequencies controls
  • Use available Hessian option
  • IR intensities option
  • Atomic masses option menu
  • Frequency scaling controls
  • Thermochemistry controls
• Surfaces controls
  • Electrostatic potential option
  • Average local ionization energy option
  • Energy units option menu
  • Noncovalent interactions option
  • Noncovalent grid density text box
  • Electron density option
  • Spin density option
  • Molecular orbitals option
  • Box size adjustment text box
  • Grid density text box
• Atomic electrostatic potential charges controls
  • Fit ESP to option menu
  • Constraints option menu
  • Grid type options
• Mulliken populations controls
• NBO analysis controls
• Multipole moments controls
• Polarizability/Hyperpolarizability controls
• NMR shieldings controls
• Atomic Fukui indices controls

Properties Table

The properties table lists all the properties that can be selected for calculation. Properties that are not available with the chosen level of theory are grayed out in the table.

To set options for a property, click the row containing the property. The controls for the property are displayed in the lower portion of the panel. If the property is not available for the chosen level of theory, the controls are displayed but are not available.

To select a property for calculation, click the check box in the Calculate column for the property.

Vibrational Frequencies Controls

Set options for vibrational frequency and thermochemistry calculations.

Use available Hessian option

Select this option if there is a Hessian available in the input file and you want to use it to calculate the frequencies. Sets ifreq=-1 in the gen section. Otherwise, the Hessian is calculated.

IR intensities option

Calculate infrared intensities. Only available for closed-shell wave functions. Sets irder=1 in the gen section.

Atomic masses option menu

Select the option for the atomic masses used in the frequency calculations. Sets massav in the gen section. The choices are:

Most abundant isotopes

Use the mass of the most abundant isotopes (massav=0). This is the default.

Average isotopic masses

Use the average atomic mass (massav=1).

Frequency scaling controls

Set options for the scaling of the frequencies. Sets isqm and scalfr in the gen section.

None

Do not scale frequencies. This is the default.

Constant

Scale frequencies using the factor given in the text box. The value can be set by choosing a method from the option menu, for which optimal scale factors have been determined.

Thermochemistry controls

Set options and values for thermochemical properties (enthalpy, Gibbs energy, entropy, heat capacity, and so on). You can calculate thermochemical properties at a range of temperatures for the given pressure.

Pressure

Enter the pressure in atmospheres. Sets press in the gen section.

Start temperature

Enter the initial temperature in K. Sets tmpini in the gen section.

Increment

Enter the temperature step in K. Sets tmpstp in the gen section.

Number of steps

Enter the number of temperature steps. Sets ntemp in the gen section.

Output units

Select an option for output in kcal/mol or kJ/mol. Sets ip28 in the gen section.

Surfaces Controls

Set options for generating plot data on a 3D grid (a "volume") that is used in Maestro to display surfaces. Plot data is written to a .vis file.

Electrostatic potential option

Calculate the electrostatic potential (ESP) on the grid (sets iplotesp=1 in the gen section).

Average local ionization energy option

Calculate the average local ionization energy (ALIE) on the grid (sets iplotalie=1 in the gen section).

Energy units option menu

Select the units used to represent the ESP and the ALIE (sets espunit in the gen section).

Noncovalent interactions option

Calculate reduced density gradient and interaction strength for visualization of noncovalent interactions (sets iplotnoncov=1 in the gen section). See Noncovalent Interactions Overview for information on how to use this feature.

Noncovalent grid density text box

Set the grid density for the reduced density gradient and interaction strength points for noncovalent interactions (sets plotresnoncov in the gen section). The default is 20 points per angstrom. A high grid density is needed for good visualization.

Electron density option

Calculate the electron density on the grid (sets iplotden=1 in the gen section).

Spin density option

Calculate the electron spin density on the grid (sets iplotden=1 in the gen section). Only available for UHF and UDFT wave functions.

Molecular orbitals option

Calculate the specified molecular orbitals on the grid. Not available for MP2 calculations. Localized orbitals are calculated if the localization was performed. GVB orbitals are the natural orbitals.

Choose the references for the molecular orbital indices from the option menus and enter the relative index in the text box.

HOMO -:  Count down from the HOMO, inclusive.
LUMO +:  Count up from the LUMO, inclusive.

Thus, From: HOMO - 0 To: LUMO + 0 includes both the HOMO and the LUMO. These controls set iorb1a and iorb2a in the gen section. The controls for beta orbitals are only available for UHF and UDFT wave functions, and set iorb1b and iorb2b in the gen section.

Box size adjustment text box

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. Sets xadj, yadj and zadj in the gen section.

Grid density text box

Enter the number of grid points per angstrom. Sets plotres in the gen section.

Atomic Electrostatic Potential Charges Controls

Set options for charge fitting to the electrostatic potential. The result is a set of atomic charges, which are displayed as properties in the Project Table.

Fit ESP To option menu

Choose option for fitting electrostatic potential. Sets icfit in the gen section.

Atomic centers

Fit to atomic centers only (icfit=1).

Atom + bond midpoints

Fit to atomic centers and bond midpoints (icfit=2).

Constraints option menu

Choose the level of charge and multipole moment constraints applied to the fit. Sets incdip in the gen section. The option All of the above applies each level sequentially (incdip=−1).

Grid type options

Select the grid type:

Spherical

Use a spherical grid, centered at the molecular symmetry center.

Rectangular

Use a rectangular grid, with spacing specified in the text box (sets wispc in the gen section).

Mulliken Population Analysis Controls

This section provides three method options for the Mulliken population analysis. Sets mulken in the gen section.

By atom

Calculate Mulliken populations by atom (mulken=1).

By atom and basis function

Calculate Mulliken populations by atom and by basis function (mulken=2).

Bond populations

Calculate Mulliken bond populations (mulken=3).

NBO Analysis Controls

There are no specific controls for NBO analysis [110, 111]. The default NBO analysis is performed. Adds an empty nbo section to the input file.

Multipole Moments Controls

There are no specific controls for multipole moments. Dipole, quadrupole, octupole and hexadecupole moments are calculated. Sets ldips=5 in the gen section.

Polarizability/Hyperpolarizability Controls

These controls allow you to specify which polarizabilities are calculated (alpha, beta, gamma) and which method is used. Not available for frozen-orbital cuts.

Property / Method option menu

Select the combination of property and method. Alpha, beta, and gamma are available with the analytic method, and alpha and beta with the finite field method. Sets ipolar in the gen section.

Finite field text box.

For finite field methods, enter the field strength in atomic units. Sets efield in the gen section.

NMR Shieldings Controls

There are no specific controls for NMR chemical shift calculations. The values reported for this property are the shieldings. The shifts must be calculated from the shieldings and a reference value. Sets nmr=1 in the gen section. Not available for frozen-orbital cuts.

Atomic Fukui Indices Controls

There are no specific controls for Fukui indices. Sets fukui=1 in the gen section.

Scan Tab Features

In this tab, you set up the coordinates for a relaxed or a rigid coordinate 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. This tab has the same features as the Jaguar Scan tab.

• Add New Coordinate section
  • Type option menu
  • Pick option menu
  • Dihedral button
• Defined Coordinates table
• Selected Coordinate section

Add New Coordinate section

Add a new scan coordinate by picking atoms 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.

Type option menu

Choose the type of coordinate to scan. The type determines the number of atoms to pick. The Z-matrix must be in the appropriate form for the coordinate type: Cartesian for Cartesian coordinates, and Z-matrix for distances, angles, and dihedrals. The coordinate types are:

Cartesian-X		X coordinate of an atom. Pick one atom.
Cartesian-Y		Y coordinate of an atom. Pick one atom.
Cartesian-Z		Z coordinate of an atom. Pick one atom.
Distance		Distance between two atoms. Pick two atoms or one bond. If you pick atoms, they need not be bonded to each other.
Angle		Angle between three atoms. Pick three atoms or two bonds. If you pick atoms, they need not be bonded to each other.
Dihedral		Dihedral angle between four atoms. Pick four atoms or three bonds. If you pick atoms, they need not be bonded to each other.

Pick option menu

Choose an object type from this option menu, then pick atoms in the Workspace to define the coordinate. When you choose from this menu, the Pick option is automatically selected. The available object types are Atom for Cartesian coordinates, and Atom and Bond for all other types of coordinates. The first atom picked remains stationary; the last atom picked is the moving atom. The atoms are marked in the Workspace as you pick them, and each coordinate is marked in the Workspace and entered in the Defined coordinates table as it is completed.

Dihedral button

Click this button to select a protein dihedral angle by name, from a list that is presented in the Dihedral Selection dialog box.

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. The columns are:

Coordinate		Labels of the atoms that define the coordinate.
Type		Coordinate type, from the Type option menu.
Steps		Number of steps to take in the given coordinate. Calculated from the values provided 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.

Selected Coordinate section

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.

Current value		Current value of the coordinate in the input structure. Noneditable.
Starting value		Initial value of the coordinate for the scan.
Final value		Final value of the coordinate for the scan.
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.

 

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the QSite - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Related Topics

• QSite - Job Settings Dialog Box