[gmx-users] Topology for a new ligand

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 11 13:33:57 CEST 2011

Kavyashree M wrote:
> Dear gromacs users,
> I wanted to know the steps to be followed
> in order to generate a topology for a new
> ligand. I went through the mailing list and
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> but was not clear.

All force fields are different, and since you haven't said which one you're 
trying to use there's nothing that anyone can tell you.  Read the primary 
literature for the force field you want to use and follow the procedure laid out 



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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