On 4/22/13 5:30 AM, Baptiste Demoulin wrote:
Hi,

You have to add an entry for the DRG residue in "aminoacids.rtp", in the
gromos folder. Instructions on this can be found in the GROMACS manual
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


This is not correct. PRODRG produces a topology (albeit a very flawed one), so there is no need whatsoever to modify .rtp files since pdb2gmx should never be involved in this workflow.

-Justin

2013/4/22 zyduscadila <haresh.aj...@zyduscadila.com>

Dear Justin thanks for your email.

I have tried those you mentioned in your email.

I have submitted molecule of interest in PRODRG and got a DRG.itp or
DRG.pdb
file.

I fired command pdb2gmx using DRG.pdb (obtained from PRODRG) using Gromos96
43a1 force field , but I received the follwoing fatel error:

"Residue "DRG" not found in residue topology database".

Let me know, how to handle this error ? please give me a brief step how to
do this ?

I hope you will give me a solution. Thanks in advance

Thanks & Regards,

HARESH AJANI




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Justin A. Lemkul, Ph.D.
Research Scientist
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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