Cerius²·Forcefield Engines

B       The Forcefield Editor

The Force Field Editor is a powerful module that allows you to edit all aspects of an existing forcefield and create new forcefields. It permits you to study, edit, and create forcefields. You can inspect or edit nearly every aspect of the forcefield: atom types, atom type rules, energy term functional forms and forcefield parameters, and the Universal forcefield's generator parameters. You can also create your own forcefield from scratch.

Although the Open Force Field module provides you with control over setting up the energy expression, the Force Field Editor module gives you direct access to the forcefield parameters themselves.

Caution

Important

This section explains

This section includes information on:

Loading and saving forcefield files

Creating and editing atom types and rules

Manipulating energy functions and parameters

Table 6 . Finding information about editing forcefields

If you want to know about:	Read:
Finding the Force Field Editor module.	Accessing the tools.
Forcefield and simulation theory.	Forcefield-Based Simulations.
Available and recommended forcefields.	Forcefield-Based Simulations.
Atom types and atom typing.	Forcefield-Based Simulations.
Formats of forcefield files.	File Formats.
Conceptual structure of atom typing rules.	Illustration, Figure 1.
How atom typing rules are implemented in the FFE interface.	Understanding rule display in the control panel.
Editing CFF and CVFF forcefields.	Documentation for the CDiscover program.
Defined or generated parameters in UFF.	Note.

Forcefield-Based Simulations (separately published by MSI) includes topics such as the functional form of various forcefields, what are atom types, what kinds of parameters are included in forcefields, rules for atom typing and for generating parameters, what forcefields are available in MSI products.

Accessing the tools

To access the C²·FFE (Force Field Editor) module, click the deck selector in the main control panel and choose OFF SETUP from the list that appears. Then click the title of the FORCE FIELD EDITOR card to bring it to the front. The deck of cards menu area should now look like this:

Loading and saving forcefield files

After you modify an existing forcefield (or create your own custom forcefield), you need to save it for it to be available for use in subsequent Cerius² sessions or after the C²·FFE module is reset.

You should already know...

Forcefield-Based Simulations, Forcefields, contains full information on what forcefields are available in MSI products.

How use file browsers is covered in Cerius2 Modeling Environment, under Finding model file(s).

Making directories in which to store files is outlined in Cerius2 Modeling Environment, under Making custom directories.

Accessing the tools

To load a forcefield, select the File/Load menu item from the FORCE FIELD EDITOR card to access the Load Force Field control panel. Alternatively, select the Load menu item from the OPEN FORCE FIELD card. If you have already loaded the desired forcefield in C²·OFF, either manually or automatically (Choosing a forcefield), you do not need to load it again before editing it.

To save a forcefield, select the File/Save menu item from the FORCE FIELD EDITOR card to access the Save Force Field control panel.

Loading forcefield files

If you want the options in the Open Force Field module's control panels to remain unchanged when you load the forcefield, click the Preferences... pushbutton in the Load Force Field control panel and then uncheck the Use options check box in the Force Field Load Preferences control panel.

To load a forcefield, use the file browser to find the forcefield filename that you want to use. Then load this forcefield by:

• Double-clicking the forcefield filename.

or:

• Choosing the forcefield filename and clicking the LOAD pushbutton.

To save your edited forcefield, use the file selector controls in the Save Force Field control panel to move through the file system to the directory in which you want to save your forcefield. Then specify a name by typing it in the file name entry box and pressing <Enter> or clicking the SAVE button.

Additional information

Please see the on-screen help for details on the functioning of each control in the Load Force Field, Force Field Load Preferences, and Save Force Field control panels.

File formats

File formats are described in File Formats.

Creating and editing atom types and rules

• Inspect atom typing rules to see how atom type assignments are made by Cerius².

• Confirm the atom types for which the forcefield has been parameterized.

• Alter the atom typing rules so that, when the Open Force Field performs automatic atom type assignment, the assignment is made exactly as you want.

• Include a new atom type in the forcefield, perhaps to accommodate an element missing from the forcefield you are using.

• Name and define all atom types in a new, custom forcefield.

• Construct atom typing rules for automatic atom type assignment with a new, custom forcefield.

This section includes information on:

Creating and editing atom types

Creating and editing atom typing rules

You should already know...

Information on atom typing is contained in Forcefield-Based Simulations under Assigning forcefield atom types and charges, and lists of atom types that are defined in various forcefields are found in Forcefield Terms and Atom Types.

Creating and editing atom types

Concepts

Five attributes are associated with each atom type in the forcefields that can be edited with the forcefield editor: element, mass, charge, hybridization, and number of lone pairs. (The lone pairs attribute is used for finding H-bond acceptors. An atom is a potential H-bond acceptor if it has some lone-pair electrons.)

How it works

Changes you make to atom types and their attributes take place immediately and cannot be undone. However, the changes do not become permanent until the forcefield file is saved (Saving forcefield files).

Accessing the tools

Select the Atom Types/Attributes menu item from the FORCE FIELD EDITOR card to access the Force Field Atom Type Attributes control panel.

Creating atom types

To create a new atom type, enter a name in the Create atom type entry box in the Force Field Atom Type Attributes control panel. Use a name that is not already used for some existing atom type.

Based on the first letters of the atom type name, Cerius² suggests possible values for its attributes, which you can edit (Editing atom-type attributes).

Editing atom-type attributes

To edit an atom type's attributes, enter the name of the atom type that you want to edit in the Current atom type entry box in the Force Field Atom Type Attributes control panel.

Tip

Edit the element name, charge, mass, number of lone pairs, and/or hybridization state as desired.

Deleting atom types

To delete an atom type, enter the name of that atom type in the Current atom type entry box in the Force Field Atom Type Attributes control panel. Click the DELETE pushbutton.

Additional information

Please see the on-screen help for details on the functioning of each control in the Force Field Atom Type Attributes and Force Field Atom Type Palette control panels.

Creating and editing atom typing rules

When is this needed?

Although the Open Force Field allows you to make atom type assignments by hand without reference to the atom typing rules (Manually assigning forcefield atom types), this is not really feasible for typing many or large structures. When custom atom typing rules have been defined for a forcefield, Cerius² automatically assigns these atom types to structures simply by searching the atom type rules.

How it works

In Cerius², atom type rules take the form of connection trees of criteria (see Figure 1). Each branch point can be defined by as many as three properties: element, hybridization, and ring membership along with an include/exclude flag.

Not all these items need be specified in a criterion. For example, if the element type is set to Any, the atom of interest may be connected to any atom, regardless of element type. If hybridization is irrelevant for the connection, it can be set to ANY.

Similarly, the ring size can also be set to ANY to include atoms in no rings and those in rings of all sizes. Or you can indicate that atoms must belong to a ring of a certain size. For example, to assign a unique atom type to an epoxide oxygen atom, a criterion specifying a ring size of 3 would be used.

Almost always, the atom described must be connected to the atom of interest in order for that atom to meet the atom type criterion. But occasionally, you may want to specify the converse, that an atom type criterion is met only if a particular atom is not connected to the atom of interest. The Atom must NOT be present check box allows you to construct this type of criterion.

Illustration

The Dreiding II forcefield uses four rules to describe the aromatic carbon atom type, C_R. As shown in Figure 1, four different environments exist for which an aromatic carbon can be assigned.

Figure 1 . Four rules for aromatic carbon type C_R in Dreiding II forcefield

See Illustration for an explanation.  

For example, if the first rule is obeyed, the C_R atom type is assigned to a carbon atom with sp² hybridization connected to any other atom with sp² hybridization, if it in turn is connected to two other atoms of any element with sp² hybridization.

Rule 3 is fulfilled if the sp²-hybridized carbon is connected to any two other atoms of sp² hybridization. For instance, Cerius² would apply rule 3 to assign the C_R atom type to the carbon atoms of benzene.

Any atom that meets all the criteria of any of the four rules is typed as a C_R atom in the Dreiding forcefield.

Understanding rule display in the control panel

Note

To examine the first rule and its implementation, use the Force Field Atom Typing Rules control panel:

• Click rule 1) in the list box. The settings shown in the Edit Rule section of the control panel show the properties of the top-level criterion (i.e., that the atom being typed must be a trigonal/sp² carbon and may or may not be part of a ring. Criterion a) in the list box indicates that this C must be bound to a trigonal/sp² atom.

• To examine the second-level criterion further, click criterion a) in the list box. The Edit Rule section shows that this atom (the one to which the atom being typed is directly bound) may be of any element and may or may not be in a ring, but must have trigonal/sp² hybridization (most of this information is already implied in the title of this criterion).

The existence of two third-level criteria in the list box means that this atom must be bound to two other atoms, both of which may be any element and must have trigonal/sp² hybridization.

• To examine the third-level criteria, click either of these criteria. No additional (fourth-level) criteria are revealed, meaning that these atoms may be bound to any other atom.

Click the up-arrow just above the list box to migrate one level up the criteria-tree so you can view the other third-level criterion.

• Click the up-arrow just above the list box until the four numbered rules appear in the list box and the entry box to the left of the arrow is empty.

• Click rule 3) in the list box. The Edit Rule section shows again that the atom being typed must be a trigonal/sp² carbon and may or may not be part of a ring.

The existence of two second-level criteria in the list box means that the atom being typed must be bound to two other atoms, both of which may be any element and must have trigonal/sp² hybridization.

• To examine the second-level criteria, click either of these criteria. This reveals no additional (third-level) criteria, meaning that these atoms may be bound to any other atom.

Prerequisites

Load the forcefield file that you want to edit by the method in Loading forcefield files or Manually loading a forcefield.

Accessing the tools

Select the Atom Types/Rules menu item from the FORCE FIELD EDITOR card to access the Force Field Atom Typing Rules control panel. Click the Palette... pushbutton in the Force Field Atom Typing Rules control panel to access the Force Field Atom Type Palette control panel. Choose the atom type whose rule(s) you want to work with by clicking the atom type name in the Force Field Atom Type Palette. This fills in the Current atom type entry box in the Force Field Atom Typing Rules control panel.

Adding a new atom-type rule or criterion

To create a new atom typing rule for an existing atom type, click the ADD pushbutton in the Force Field Atom Typing Rules control panel. Click the name of the newly added rule in the list box, then edit the top-level rule (Editing an atom-type rule or criterion).

If you need to create a new atom type, please see Creating atom types before attempting to create rule(s) for it,

To create criteria (second- and third-level "rules") for an existing atom typing rule, select the rule by clicking it in the list box in the Force Field Atom Typing Rules control panel. Navigate the criteria tree (if necessary) to find the level at which you want to add a lower-level criterion (or another lower-level criterion, to form a branching criteria tree). Click the ADD pushbutton to add a new criterion. Select and then edit the criterion (Editing an atom-type rule or criterion).

Remember

Editing an atom-type rule or criterion

To edit an atom typing rule or criterion, select the rule you want to edit by clicking it in the list box in the Force Field Atom Typing Rules control panel. Navigate the criteria tree (if necessary) to find and select the criterion you want to edit.

Tip

Edit the rule or criterion by changing the settings of controls in the Edit Rule section of the control panel.

Deleting an atom-type rule or criterion

To delete an entire atom typing rule or a criterion (including all lower-level criteria that lead from it), find and then select the rule or criterion by clicking it in the list box in the Force Field Atom Typing Rules control panel. Click the DELETE pushbutton.

Additional information

Please see the on-screen help for details on the functioning of each control in the Force Field Atom Typing Rules control panel.

Manipulating energy functions and parameters

• Confirm the energy terms with which the forcefield has been parameterized and check functional forms and parameters for specific sets of atom types.

• View the Universal forcefield's (UFF) single-atom-type parameters used by its generator.

• Adjust individual parameters in UFF or other Cerius² forcefields, perhaps to improve the agreement of calculated results with experimental data.

• Choose a different functional form (as well as parameters) for the equation used to calculate an energy interaction.

• Select the functional forms and parameters for all types of energy interactions you want to include in a new, custom forcefield.

This section includes information on:

Editing energy functions and parameters

Changing UFF's generator parameters

You should already know...

Forcefields and Forcefield Terms and Atom Types of Forcefield-Based Simulations contain information on forcefield energy terms, what energy terms are included in which forcefields, and their functional forms.

Atom-type definitions can be understood by examining the Force Field Atom Type Attributes (Creating and editing atom types) and Force Field Atom Typing Rules (Creating and editing atom typing rules) control panels.

Editing energy functions and parameters

How it works

Energy terms (also called interactions) are specified according to atom type names. The generic atom type X can be used to indicate any atom type.

For example, if the atom types X, C_R, and X are listed for an angle-bending energy term, then all valence angles with C_R as the central atom are governed by the same energy term (and parameters), unless a more specific energy term has been parameterized. So, if the model contains the angle C_R-C_R-C_R, Cerius² looks for parameterized energy terms in the order listed below and uses the first one found (combinations 2 and 3 are equivalent):

1.   C_R, C_R, C_R

2.   X, C_R, C_R

3.   C_R, C_R, X

4.   X, C_R, X

5.   X, X, X

Technical notes

Any energy terms that are available in the current forcefield may be edited. If an energy term is not included in the forcefield definition, no forcefield types are found in the list box in the control panel relevant to that interaction.

If an interaction is of the same form for all atom types, only X entries are contained in the list box in the control panel relevant to that interaction.

Important

Accessing the tools

Select the desired item from the Energy Terms menu in the FORCE FIELD EDITOR card to access control panels for each type of energy term. (This includes all items in the Energy Terms menu except for the Energy Terms/Universal menu item, since UFF is a conceptually different forcefield from all the others and is thus parameterized and edited differently, Changing UFF's generator parameters.)

Creating energy terms

You can define specific energy terms for specific sets of atom types that are not included in the predefined energy terms. To do this, enter the atom types in the Current Function entry boxes and set the Function popup to the desired functional form. Edit the parameter values as described under Editing energy terms.

Note

Inspecting energy terms

Specify which term to examine by choosing the appropriate control panel (Bond Stretch, Angle Bend, etc.) and then selecting the appropriate set of one or more atom types from the list box in the control panel (see Tips).

The interaction energy function and the function parameters for the chosen atom type pair are displayed in the lower section of the control panel.

Editing energy terms

Specify which term to edit by choosing the appropriate control panel (Bond Stretch, Angle Bend, etc.) and then selecting the appropriate set of one or more atom types from the list box in the control panel.

Tips

To change the functional form of the chosen energy term, set the Function popup as desired. (There is no "undo" function in these control panels, so you need to remember what the original functional form was, if you want to return to it.)

When you change the functional form, Cerius² displays the appropriate parameter types and assigns default values for them. Generally you would want to change these values.

To change the parameters for the energy term, edit the values in the entry boxes in the lower section of the control panel.

Your changes take place immediately but do not become permanent until you save the edited forcefield (Saving forcefield files).

Ignoring or removing energy terms

Specify which term to ignore (i.e., specifically set the energy term to zero) by choosing the appropriate control panel (Bond Stretch, Angle Bend, etc.) and then selecting the appropriate set of one or more atom types from the list box in the control panel. Set the Function popup in the control panel to IGNORE.

To completely remove an energy term from your forcefield, click the DELETE pushbutton in the control panel. This action sets the Function popup in the control panel to UNDEFINED (which means that there is no functional form for this term).

However, interactions for the set of atoms for which a specific energy term has been deleted may still be calculated, if an appropriate energy term for atom sets that include X atom types (that is, any atom types) is defined. For example, if the C_R-C_R-C_R angle energy term is undefined, the angle energy could be calculated according to the function and parameters for the X-C_R-X atom combination. If you really do not want to calculate energy for the C_R-C_R-C_R angle-bending energy at all, you need to ignore it (Ignoring or removing energy terms), which sets this angle energy term to zero.

Additional information

Please see the on-screen help for details on the functioning of each control in the control panels used for editing energy terms.

Changing UFF's generator parameters

Concepts

Generator parameters are single-atom-type parameters that are used to generate the forcefield parameters that are used in the terms of the energy expression.

How it works

UFF combines the generator parameters using a prescribed set of equations to generate forcefield parameters for bond, angle, torsion, inversion, van der Waals, and Coulomb energy terms (Rappé et al. 1992).

Note

Accessing the tools

Select the Energy Terms/Universal menu item from the FORCE FIELD EDITOR card to access the Universal Force Field Generator control panel. Click the Palette... pushbutton in the Universal Force Field Generator control panel to access the Force Field Atom Type Palette control panel. Choose the atom type whose generator parameters you want to examine or edit by clicking the atom type name in the Force Field Atom Type Palette. This fills in the Current atom type entry box in the Universal Force Field Generator control panel.

Editing generator parameters

Simply enter your desired values for the generator parameters in the appropriate entry boxes in the Universal Force Field Generator control panel.

Your changes take place immediately but do not become permanent until you save the edited forcefield (Saving forcefield files).

Additional information

Please see the on-screen help for details on the functioning of each control in the Universal Force Field Generator control panel.