[gmx-users] PRODRG server

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 19 12:57:54 CET 2011

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:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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