[gmx-users] Adding missing heavy atoms
jalemkul at vt.edu
Sun Jul 12 04:35:52 CEST 2015
On 7/11/15 1:03 AM, prasun kumar wrote:
> Dear All
> I have generated the base atoms of nucleotides in a structure, but it does
> not have sugar and phosphate atoms. Is there any method by which I can add
> them appropriately (either in A or B form)
If you already have the base configuration, you cannot choose between A- and
B-form helices; the stacking of each is different.
I suggest NAB from AmberTools. It is extremely is easy to use for generating
structures of any geometry and sequence.
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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