[gmx-users] About a "general" force field

[David van der Spoel]

Francesco Pietra wrote:
> Hi:
> I come from Amber world; am an organic chemist. Therefore, besides the
> biopolymer, the "organic molecules", in particular tricky natural products are
> in my forefront list.
> 
> I am used to GAFF ff and Antechamber tool to generate files to carry out MD or
> docking (DOCK program).
> 
> Now my problem is to carry out a cluster analysis for a long trajectory for
> which I have both Amber files and pdb. Thus, I want to try trjconv etc.
> 
> As I am at Debian Linux, it was easy to install gromacs as a deb package. Did
> that on i386, though, in I succeed in using gromacs, I'll install it on a
> parallel dual-opteron machine from the latest version (in Debian it is for
> last, 3.3.1.-4). I rely on OpemMPI 1.2.3 and want to use general libraries from
> Debian or elsewhere.
> 
> I would appreciate to be directed to documentation on how to deal with the
> "organic molecule" (thus not simply fatty acids,. or the like) in gromacs. As I
> am familiar with ab initio on NWChem, I could get parameters from ab initio,
> though generally it would be too time consuming for my type of interests.
> 

You can keep using gaff parameters with the amber ff in gromacs. Look 
for the ambconv script to convert amber topologies.

> Thanks
> 
> francesco pietra
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se