[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.
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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