[gmx-users] pdb2gmx error
acootbrett at yahoo.com
Mon Apr 2 02:48:07 CEST 2012
I have renumbered the residues. Both 2 chains start from Resis 1. The pdb2gmx still does not work. The fifth residue in the chain A is Val, no CG atom. The fifth residue of chain B is Gly, no CG atom.
What is 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 10:32 AM
Subject: Re: [gmx-users] pdb2gmx error
On 2/04/2012 10:26 AM, Acoot Brett wrote:
>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.
>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:
>>I just run a pdb2gmx of a protein, the error message is "
>>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
>>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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