mohsen ramezanpour wrote:
Dear All
I generated toplogy file for a drug by PRODG server.
How can I validate it?
i looked at these links but there are not a way for doing that.
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
thanks in advance
The Gromacs site is not going to be a comprehensive, how-to-do-everything site.
If you're using a certain force field, you should have based that choice on an
understanding of how that force field was derived, its inherent assumptions,
limitations, etc. Refer to the original literature for whichever parameter set
you want to use for parameterization methodology.
That said, Gromos parameterization is a bit vague, although the basics are
certainly described in the literature. Did you read the paper linked from
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips? There are tips
there. Another of my papers (shameless self-promotion, sorry) has an example of
how I treated one particular molecule, as an example:
http://pubs.acs.org/doi/abs/10.1021/bi1000855
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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