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

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 7 12:54:40 CET 2008

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
>       ____________________________________________________________________________________
> Looking for last minute shopping deals?  
> Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list