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

[Anurag Dobhal]

Thank You




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


On Fri, Jun 17, 2016 at 5:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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