Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 8 12:34:46 CEST 2009
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
> -----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
> Gromacs. Specifically, the first error message located under the pdb2gmx
> heading here:
>> See you.
>>> 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
>>> 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
>>> using PRODRG?
>>> Chanel King
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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