[gmx-users] Adding missing heavy atoms

[prasun kumar]

Dear Justin and tarak

Thanx alot for the reply

If I have base atoms, so I have stacking information also.
I was curious to know whether by changing the forcefield information will
help me or not.
For example, when I need ADNA, I will use some other information related to
it and like that it continues for BDNA or ARNA

Regards

PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success

On Sat, Jul 11, 2015 at 10:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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