[gmx-users] Fw: protein-DNA complex

[Mahboobeh Eslami]

     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GROMACS rely on very outdated AMBER nucleic acid force fields, and should be 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

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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