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.
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