[gmx-users] I need ligand topology file

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 17 18:19:20 CET 2011

ajaniharesh at gmail.com wrote:
> Hello everyone,
> I am using gromacs 4.5 version.
> I am from cadila healthcare ltd.
> I have protein with ligand file. But I can't submit prodrg server bcoz this confidancial data.
> I want to genrate .itp without using prodrg server.
> Have any way that i can genrate .itp file.
> Plz help me out.

Your best resources are Chapter 5 of the manual and the primary literature for 
your chosen force field.  There are a couple of user-contributed programs posted 
on the Gromacs site that will produce topologies, but nothing should supplant a 
proper parameterization procedure.





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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