Re: assigning atom type for parameterization

From: Jan Saam (
Date: Fri Sep 08 2006 - 20:21:32 CDT

Hi Dhiraj,
there is no unique correct way to assign the types, but you can follow
this simple guideline:

Try to find an equivalent existing type of the same chemical element,
Paratool lets you pick that from a list. Many of the types for a certain
element have the same VDW params, e.g. CD and CC.
C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
                ! NMA pure solvent, adm jr., 3/3/93
CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
                ! benzene (JES)
CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
                ! adm jr. 3/3/92, acetic acid heat of solvation
CD 0.000000 -0.070000 2.000000 ! ALLOW POL
                ! adm jr. 3/19/92, acetate a.i. and dH of solvation
The reason why there are two types is that they are used in different
contexts so that you can for instance distinguish dihedrals including CC
or CD.
Which type to use has to be decided using chemical insight. Just try to
find the most similar atomtype by comparing structures where it appears.
Factors influencing this similarity are for example hybridization state,
polarization, same neighboring atoms.
Always try to use an existing atom type, unless you end up with bonded
parameters that are not equivalent enough. In the latter case you just
change the type name, but keeping the VDW params. In case there is no type
for the atom's chemical element you can use VDW parameters from the
"Universal force field" they are at the end of the list. You can of course
change the predefined typename if you want.

Assinging types implies the automatic assignment of bonded parameters for
which all types are known and for which a matching entry could e found in
the currently loaded parameter files.

I hope this helps.

PS. I'm working on the Charmm charges problem, both, bugfixes and docs...

Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin

+49 30 450-528-446

> does any one know how to assign atom type during parameterization and
> is the basis of atom type in charmm force field? I am trying to
> parameterize
> a molecule but do not know how to assign atom type? is there any rule
> assigning atom type or it is based on your own choice?
> thank you for your help.
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153

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