[gmx-users] Regarding OPLSAA

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 29 13:24:39 CEST 2011

Ravi Kumar Venkatraman wrote:
>     Dear All,
>                  I am using OPLSAA forcefield for generating methanol
>     solvent box. The methanol.pdb/methnaol216.gro that is available in
>     XXXX/tutor directory of gromacs is for united atom. Please tell me
>     where I can get the methanol coordinates for All Atom. Can I use
>     *.gro file that can be got from PRODRG server.

You can obtain an all-atom coordinate file from PRODRG, but do not use the 
topology it gives you.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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