[gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

[Justin Lemkul]

On 6/17/16 4:42 AM, Anurag Dobhal wrote:
> Dear Gromacs users,
>
> I want to simulate Guanine ( a nitrogenous base) molecules in water using
> OPLS AA force field.
>
> I used the "opls aa"  parameters from atomtypes.atp ((JACS,113,2810(1991)).
> on calculating the total charge of one molecule it comes to a negative
> value.

The .atp file has no charges.  The charges found in ffnonbonded.itp also mean 
nothing.

> dose it means that guanine has negative charge ?

Not as just the base.  The nucleotide form is of course anionic.

> should I continue with thae same  parameters or change them to bring the
> total charge of the molecule to zero.
>

You should be sure you have a proper model with a reliable source of parameters. 
  Stripping the base out of a nucleotide also requires the introduction of an H 
to fill the valence at the glycosidic linkage.  Charges may differ as a result 
of such a change.

-Justin

> Thank You for your help
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
>

-- 
==================================================

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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