Smith, Chanel Chonda wrote:
Hello,
I have recently made a pdb file using the Dundee PRODRG server.
However, when I try to use this pdb in gromacs, I receive an error message
that states: "DRG is not in the topology database." I have tried to use the
available tutorial to solve this issue, but with not much success. Could
anyone give me a step by step procedure so that I can use the pdb I have made
using PRODRG?
The purpose of PRODRG is to generate the topology, such that you don't have to
pass it through pdb2gmx. If the molecule doesn't exist in the force field .rtp
file, then you will get this error. John Kerrigan's tutorial explains how to
use the PRODRG topology within your system .top quite clearly.
Be advised that the charges and charge groups produced by PRODRG are often
unsatisfactory, requiring manual modification and validation.
-Justin
Thanks,
Chanel King
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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