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

[Anurag Dobhal]

Dear Justin,

I have already added the H to the guanine molecule striped from the
nucleotide.
The charges given in the ffnonbonded.itp for all the atoms of guanine
(Including the H on N9) do not add to zero.






*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Fri, Jun 17, 2016 at 3:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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