[gmx-users] Fw: protein-DNA complex

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Mon Feb 29 12:04:03 CET 2016

     On Monday, February 29, 2016 12:55 PM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:

 dear Justinthanks for your answerI have another question. Which of the following items is better in mdp file for the equilibration and MD production steps?
tc-grps       = Protein-DNA    SOL-ION
or tc-grps       = Protein   DNA   SOL-ION
Sincerely thank youbest 

    On Saturday, February 27, 2016 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:


On 2/27/16 3:03 AM, Mahboobeh Eslami wrote:
> hi all I want to do molecular dynamics simulations on protein-DNA complex.
> should  the simulation of  protein-DNA complex be done like the
> protein-protein complex? or is it  better to select different force field for
> protein and DNA separately in MD simulation of protein-DNA?  How is simulated
> protein-DNA complex? Thanks so much for your help.

It's just like simulating any other molecule-in-water system, be it a single or 
multiple proteins.  You shouldn't choose different force fields, because mixing 
and matching is generally a very (very very very) bad idea.  All modern 
biomolecular force fields support proteins, DNA, and more.  Read up on the 
quality of each before moving on; for instance, the AMBER implementations in 
GROMACS rely on very outdated AMBER nucleic acid force fields, and should be 
replaced with the more recent parameter sets. I believe some of these are 
available on the GROMACS user contributions page, but the validation issues, 
AFAIK, were never resolved, so check carefully...



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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