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.
Mark
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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