[gmx-users] sample working DNA file?

Justin Lemkul jalemkul at vt.edu
Wed Aug 12 13:36:23 CEST 2015

On 8/12/15 6:07 AM, toannt wrote:
> Hi all,
> I have problems with a simple setup of DNA system. I try some programs to
> generate DNA pdb file. Some pdb output doesn't work. Some requires a lot of
> manual edits. I finally got a pdb file working but I still have some problems
> with long "bonds". Does anybody have a sample working DNA pdb file and could
> share with me?

DNA structures unfortunately do not always have the same level of standardized 
nomenclature as proteins, so some manual editing or use of .r2b files is needed, 
especially as naming also varies among force fields.  A sort of bulletproof DNA 
structure is PDB 1BNA (or really anything else that isn't missing any atoms).



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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