[gmx-users] regarding pdb2gmx

Justin Lemkul jalemkul at vt.edu
Sat May 30 16:26:18 CEST 2015

On 5/30/15 10:24 AM, soumadwip ghosh wrote:
> Thanks Justin for your insights.
> So when I am making the topology of DNA via ppdb2gmx using CHARMM, the
> parameters in the .itp files are not adequate and I should place them
> manually everytime I make a molecule topology with pdb2gmx? In some of
> my previous works actually the DNA molecule gave outcomes which were
> pretty much expected. So, just like I have put all the missing
> parameters in the .cnt.itp file should I do the same with the dna.itp
> generated by pdb2gmx in order to ensure correct interactions?

No.  The parameters for DNA exist in the force field, so grompp looks them up, 
finds them, and carries on happily.  Again, this is how all the force fields 
work except GROMOS.



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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