6. Creating a new force field template

With ATDL (Atom Type Description Language), you can expand VEGA with new atom types and/or with new force field templates. Actually, VEGA supports the following templates:

Force Field

Package

AMBER

Amber

BROTO Broto and Moreau atom types for logP calculation
BOND Used by VEGA to calculate the bond types (single, double, partial double and triple).
CFF91 CFF91 by Accelrys
CVFF CVFF by Accelrys

CHARMM

Accelrys Quanta/CHARMm

CHARMM22_NA CHARMM 22 for nucleic acids
CHARMM22_LIPID CHARMM 22 for lipids
CHARMM22_PRO CHARMM 22 for proteins
CRIPPEN Ghoose and Crippen atom types for logP calculation
GRID Grid
HBOND H-bond atom types (for internal use)

MENG

By Elanie C. Meng and Richard A. Lewis

MM+ MM+ atom types
MM2 MM2 by N .L. Allinger
MM3 MM3 by N .L. Allinger

TRIPOS

Sybyl by Tripos

UNIV

For Gasteiger atom charges attribution

For each force field, the description of atom types is stored into a file with uppercase name (corresponding to the force field name) and .tem lowercase extension (e.g. AMBER.tem, CVFF.tem, etc). All template files are placed in Data directory. Please remember that the .tem extension is for all VEGA templates and not for force field only.

In all template files the first column can contain special control characters:

Character

Description

;

Comment line marker

#

Keyword or command marker

The first line must contain a keyword needed for file type recognition. For force field it must be:

#TemplateFF [TEMPLATE_NAME] [VERSION]

where TEMPLATE_NAME is the name of the force field template and VERSION is the revision number.

e.g. #TemplateFF CVFF 3.0

After this keyword, you can place the atom type description. The first column is the atom type name (max 8 characters), the second is the atom description in ATDL and the third contains the description of bonded atoms (also in ATDL).
In this last column, each group of atoms limited by parenthesis contains all atoms bonded to precedent atom:

C-300 (O-100 O-100)

This line describes a carboxylic carbon: a sp2 carbon bonded to two oxygens making one bond only. More than one levels of parenthesis can be used for complex description of atom types:

C-300 (O-100 O-200 (C-900) C-900)

This line describes a carbonylic carbon of an ester group, bonded to a generic carbon. The O-200 is also bonded to a generic carbon.
Please remember that VEGA reads the line from left to right and thus the more restrictive atom description must placed in more left side of line:

C-400 (C-300 X-900 X-900 X-900)

And not:

C-400 (X-900 X-900 C-300 X-900)

If VEGA finds a C-300 as first or second atom bonded to a sp3 carbon, this is recognized as a more generic X-900 atom and can’t be reassigned to the next more specific description.
The description sequence of each atom type goes from more to less specific, from upper to lower line:

cn C-400 (N-300 X-900 X-900 X-900) more specific
c C-400 (X-900 X-900 X-900 X-900) less specific

If the order of this two lines is swapped, when VEGA finds a carbon bonded to a sp3 nitrogen, the atom type recognized is a generic c an not a cn.

 

6.1 ATDL atom description

 

ATDL

Each atom can be defined by a five character string. The first two characters are the element symbol of atom. If the element symbol is one character only, the second character must be a dash (-). For a better description, special element are included: X for any atom and # for heavy atom.
The third character is the bond order: use values from 1 to 6 for real bond order, for non-bonded atom and 9 for a bonded atom with a non-specified bond order.
The fourth character is the ring indicator: use values from 3 to 6 if the atom is a 3 to 6-ring member, 0 for a non-ring member atom and 9 for a non-specified ring atom.
The fifth character is the aromatic indicator: 0 for non-aromatic atom and 1 for aromatic atom.

Examples: