[gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations

Justin Lemkul jalemkul at vt.edu
Thu Mar 17 15:04:32 CET 2016

On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:
> Dear Gromacs Users,
> I have to run a protein-ligand system. I am using CHARMM36 ff for the
> simulation. For generating the parameters for the ligand molecule I used
> the forcefield development toolkit of vmd, which gives CHARMM compatible
> parameters.
> But, I am unable to understand how should I include the parameters I had
> obtained. I went through the tutorial files which shows an example of
> PRODRG server for generating the itp file, but my ligand contains metal
> atoms. I would appreciate if somebody could suggest me how to solve this.

What are the ligands?  What metal?

Don't use PRODRG; it's only intended for GROMOS force fields (and even then, the 
topologies need a lot of work).



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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