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_PRO | CHARMM 22 for proteins |
CRIPPEN | Ghoose and Crippen atom types for logP calculation |
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 cant 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.
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: