[gmx-users] pdb2gmx error

Acoot Brett acootbrett at yahoo.com
Mon Apr 2 02:26:12 CEST 2012

Hi Mark,
As for the pdb2gmx is the first step, there is still no gro file and rtp file produced by this step.
In addition, in my protein the first residue is Resi 71, which means there is no resi 5 at all.
I am looking forward to getting your suggestion.

 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 " 
>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.

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