[gmx-users] DNA topology error

Justin Lemkul jalemkul at vt.edu
Tue Jul 11 22:38:31 CEST 2017

On 7/11/17 3:40 PM, maria khan wrote:
> dear Mark Abraham
> According to my error like  """Residue 9 named DG of a molecule in the
> input file was mapped to an entry in the topology database, but the atom
> O5' used in that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed."""
> if O5' can be set in pdb manually,then how  the other values of
> cordinates   (figures) can be provided manually,as these values are
> experimental.

Regular B-form DNA has a predictable structure.  If yours is incomplete, there 
are a variety of utilities that you can use to model in the missing atoms.  Just 
Google around.



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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