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.
Thanks
francesco pietra
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