[gmx-users] asking for N and C termini for DNA and giving error

[Justin Lemkul]

On 3/16/14, 11:35 PM, Sucharita Dey wrote:
> Hello,
> Thanks Justin.
> Since my protein has a modified DNA residue (methyl cytosine) I have copied the "gromos53a6.ff" folder as well as the "residuetypes.dat" file in my working directory and modified them, where I have inserted my modified DNA residue as DNA and also have renamed DADE, DTHY ... as DNA. Within "gromos53a6.ff", following "Adding a new residue" from gmx-tutorial, I have modified .rtp, .hdb, atomtypes.atp, and residuetypes.dat. In the rtp, hdb files as well DNA is written as DADE, DTHY.... And I am choosing this force field from the current directory while running pdb2gmx. It is not giving error for the modified residue but giving error for DNA terminal. Am I missing anything for which it is not identifying the DNA as "DNA"?

The Gromos96 53A6 force field does not have termini database entries for DNA or 
RNA, so the nucleic acids are not fully functional.  I don't know why you chose 
this parameter set, but the nucleic acid parameters are far surpassed (in terms 
of quality) by other force fields like AMBER and CHARMM.  I would recommend you 
use one of those, instead.  They are also fully functional within Gromacs.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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