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"
<[EMAIL PROTECTED]> wrote:
Quoting Shankar Prasad Kanaujia <[EMAIL PROTECTED]>:
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
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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