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.
Cheers,
Acoot
________________________________
From: Mark Abraham <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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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