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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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