[gmx-users] AMBER (parm96) force field

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 3 16:07:29 CET 2001

On Mon, 3 Dec 2001, Filip Ryjacek wrote:

>Dear GROMACS users,
>I wonder if anybody has ported Cornell et al. 1996 (parm96) force field to
>GROMACS. In my opinion, reformating of parm96.dat to ff??.atp, ff??.bon.itp
>and ff??nb.itp is easy, but residue databases ff??.rtp....it is different
>question. I need residues for DNA canonical bases....can anybody help?
>P.S. I just started work on topology/coordinate convertor (AMBER --> GROMACS).
>It will create GROMACS .top or .top and .itp files from AMBER .top files.
>If you want to join, you are welcome. Programming language is plain C.
Have you checked whether there is a one to one translation of atom types
from amber to gromos force field? If so it should be quite easy...

If we have a list that contains the following:
Residuename	Atomname	Atomtype	Charge

then it would be quite straightforward to generalize. THe only cumbersome
point is then the termini for a protein (DNA).

THis could be implented in pdb2gmx without too much effort.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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