[gmx-users] Force field For Protein-Ligand Complex
jalemkul at vt.edu
Mon Feb 2 13:53:59 CET 2015
On 2/2/15 3:36 AM, neha bharti wrote:
> Hello All
> I have to perform molecular dynamics simulation of protein-ligand complex
> in water.
> Initially I tried using gromos force field but there is some problem in its
> ligand itp file which is generated by PRODRG server. I also tried it with
> the help of ATB but again its giving error.
> Can I use CHARMM 27 or Charmm 36 force field for the same. Is there any
> reference paper??
You can do any protein-ligand complex simulation with any force field; it's all
just a matter of how easy it is to generate ligand parameters. For CHARMM, use
the ParamChem server. There are analogous servers and programs for AMBER, as well.
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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