[gmx-users] ligand topology

Justin Lemkul jalemkul at vt.edu
Tue Aug 1 00:53:32 CEST 2017

On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> Dear Sir
> I am new for protein-ligand complex. I want amber force field (ff03) for my
> protein, tip3p for water model and gaff (General Amber force field) for
> ligand. I do not know how to produce gaff force field from pdb and then
> convert for gromacs topology.
> I have tried ff03 with gromos ligand topology and tip3p water model
> it gives me the error:
> atomtype OM not found
> and when I have tried ff03 with gromos topology and spc water model it
> gives me the error like:
> atomtype HW not found.
> Can anyone help me about it?

You can't mix and match force fields; it's fundamentally wrong.  You need to 
develop ligand parameters that are consistent with the parent protein force 
field.  Various tools exist for different force fields, with varying degrees of 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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