AMBER Archive (2006)

Subject: RE: AMBER: Organic molecules

From: Ross Walker (
Date: Tue Feb 14 2006 - 11:44:25 CST

Dear Marie,

> I'd like to know if it's possible to work on an organic
> molecule (not a protein)
> with a force field different than leaprc.gaff?

In principle yes. Although you will have to build a unit (residue) for the
organic molecule and specify atom types, charges and force field parameters.
This is typically what is done with co-enzymes such as NADH.

If you would like to simulate a molecule using your own parameters (and
charges) instead of the GAFF ones then the easiest way to do this is
probably to use antechamber to create your molecule as if it were using the
gaff force field. Then you can load the unit in xleap and edit it to to
change the atom types and charges. You can then provide a frcmod file
containing the parameters for the atom type combinations you specified.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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