[gmx-users] PRODRG

[Smith, Chanel Chonda]

In the drug-enzyme tutorial it says that the crude was refined using a
certain force field, SD, and CG. How was this accomplished?

-----Original Message-----
From: gmx-users-bounces at 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_quintero at 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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> 
> 
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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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