[gmx-users] sample working DNA file?
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
More information about the gromacs.org_gmx-users