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

[Justin Lemkul]

On 6/17/16 6:26 AM, Anurag Dobhal wrote:
> 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.
>

As I said, those charges mean nothing.  You should find force field parameters 
specifically for the base from published literature or from another force field. 
  AMBER and CHARMM are much better choices than OPLS-AA for nucleic acids and 
their components, anyway.  CHARMM has a topology for all bases as part of the 
stock force field.

-Justin

>
>
>
>
>
> *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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-- 
==================================================

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

==================================================