[gmx-users] GTP topology generation in OPLS-AA force field

[TJ Piggot]

Bear in mind that parameterising a new molecule is an advanced topic. Maybe 
an easier solution would be to use another forcefield which already has a 
GTP topology. For example the amber forcefields I know to have GTP 
parameters available, all you would have to do is to convert them into 
GROMACS format.

Tom

--On Wednesday, April 30, 2008 06:49:35 -0400 "Justin A. Lemkul" 
<jalemkul at vt.edu> wrote:

> Quoting Shankar Prasad Kanaujia <spk at rishi.serc.iisc.ernet.in>:
>
>> Dear gmx-users,
>> I want to run MD for my protein with GTP compound.
>> I am using OPLS-AA force field. How can I generate
>> the topology file for GTP in OPLS-AA force field ?
>
> Derive parameters consistent with the methods used to generate the
> original force field.
>
> http://wiki.gromacs.org/index.php/Parameterization
>
> -Justin
>
>>
>> Thanking you all for your kind support and suggestions.
>>
>> ---
>> Yours Sincerely,
>> Shankar Prasad Kanaujia
>> Research Student
>> C/O - Dr. K. Sekar
>> Bioinformatics Center, Department of SERC
>> IISc, Bangalore - 12, INDIA.
>> Office Phone: 2469, 3059
>> Mobile: 9845631581
>>
>>
>>
>> --
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>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.