[gmx-users] PRODRG

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 7 16:59:01 CEST 2009

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.


> 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


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