[gmx-users] Protein-DNA_ligand simulation.

Justin Lemkul jalemkul at vt.edu
Tue Nov 22 21:24:18 CET 2016

On 11/22/16 2:06 PM, maria khan wrote:
> Dear Gromacs users.
> Can gromacs is used in Protein -DNA-ligand simulation??f it is  used, which
> forcefield will be used.??

Just about any will work, but CHARMM and AMBER are most commonly used for 
systems like these.  You should investigate (in the literature) the suitability 
of current parameter sets in light of how they might affect properties of 
interest (e.g. AMBER99 is a bad choice for DNA because it distorts over time, 
but more recent parmbsc1 is good, similarly CHARMM36 is vastly better than 
CHARMM27 for nucleic acids).

> what will be the method for that type of simulation.kindly answer me in
> detail.

Simulating a protein-DNA complex is no different from a protein in water. 
You've got a biomolecule in aqueous solvent.  The protocol is generally the same.



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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