[gmx-users] PRODRG

[Justin A. Lemkul]

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-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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> 

-- 
========================================

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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