Smith, Chanel Chonda wrote:
In the drug-enzyme tutorial it says that the crude was refined using a
certain force field, SD, and CG. How was this accomplished?
Then parameters from that force field (like charges and charge groups from
analogous functional groups) were probably assigned, followed by energy
minimization.
-Justin
-----Original Message-----
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Wed 10/7/2009 1:11 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PRODRG
jorge_quint...@ciencias.uis.edu.co wrote:
Hello Chanel
Could you send a copy of the PDB file. I think that the error is related
with label atoms included in each force fiel parameter.
More likely this is yet another case of a common misconception about how to
use
Gromacs. Specifically, the first error message located under the pdb2gmx
heading here:
http://www.gromacs.org/Documentation/Errors
-Justin
See you.
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?
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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