[gmx-users] Adding missing heavy atoms

[Justin Lemkul]

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.

http://ambermd.org/tutorials/basic/tutorial1/section2.htm

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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