[gmx-users] Adding missing heavy atoms

[Justin Lemkul]

On 7/22/15 1:00 PM, prasun kumar wrote:
> 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
>

Any force field that needs to use conformation-specific parameters to enforce 
some geometry is a bad force field.  Thankfully, I know of no force fields that 
do this.  Proper force fields will correctly sample conformational fluctuations 
that reflect the real ensemble of the biomolecule in solution.

-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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