[gmx-users] pdb2gmx error

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 2 02:32:30 CEST 2012

On 2/04/2012 10:26 AM, Acoot Brett wrote:
> Hi Mark,
> As for the pdb2gmx is the first step, there is still no gro file and 
> rtp file produced by this step.

I didn't suggest you look at *output* files.

> In addition, in my protein the first residue is Resi 71, which means 
> there is no resi 5 at all.

The fifth in the sequence, then. Perhaps with a terminal residue. After 
all, you haven't told us anything about what you're doing.


> I am looking forward to getting your suggestion.
> Cheers,
> Acoot
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Monday, 2 April 2012 10:22 AM
> *Subject:* Re: [gmx-users] pdb2gmx error
> On 2/04/2012 10:19 AM, Acoot Brett wrote:
>> Dear All,
>> I just run a pdb2gmx of a protein, the error message is "
>> Fatal error:
>> Atom CG is used in an interaction of type atom in the topology
>> database, but an atom of that name was not found in residue
>> number 5."
>> According to the sugestion I have tried to find the reason in "
>> http://www.gromacs.org/Documentation/Errors"
>> But in that part of Document no this error was explained.
>> I am looking forward to getting an explaination from you.
> Like it says, look at residue 5 in your .gro and .rtp input files. 
> They need to match well enough.
> Mark
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