[gmx-users] sample working DNA file?
nabajyoti.goswami at gmail.com
Thu Aug 13 10:28:58 CEST 2015
Try using xleap of AmberTools.
On Wed, Aug 12, 2015 at 5:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> manual edits. I finally got a pdb file working but I still have some
>> with long "bonds". Does anybody have a sample working DNA pdb file and
>> 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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