You still haven't provided all of the relevant information. For
example: what ff are you using? But please don't just sent that
information now... better for you to read about how to develop a good
post and next time be suer to include enough information that we could
reproduce the problem if we tried.
In any event, the OXT atom is not recognized by your force field.
Depending on how many oxygen atoms you have in your final LEU residue,
you should rename it as you see based on either ff*.rtp or ff*-c.tdb.
I would personally keep only a single oxygen in your c-term LEU and
rename it "O". You can add back the original coordinates by hand to
the .gro if you wish. I am not sure if pdb2gmx can handle being
supplied with the coordinates of the heavy atoms for the termini or
not. In any event, this will let pdb2gmx produce the .top/.itp for you.
I am a little surprised that you are running into this because
xlateat.dat should allow renaming of OXT --> O automatically but
perhaps the problem is that you are supplying both O and OXT? (but
then again you didn't provide the coordinates of the c-terminal
residue).
To be honest I have not struggled with this much because I have always
just done as I suggested to you above and it works fine. I guess it's
possible that you are using a very old version of gromacs (but then
again you didn't say what version you are using).
Chris.
Message: 4
Date: Tue, 06 Sep 2011 22:35:09 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] atom type OXT
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4E66137D.9040103 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 6/09/2011 11:39 AM, Sweta Iyer wrote:
Hi all,
I have been trying to pdbgmx my protein to obtain the gro and top files
as follows:
pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter -ignh
However, I get an error message that states:
Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
while sorting atoms
We don't know what termini you are choosing (or want), so it's hard to
help. See also
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains
Mark
Hi,
I chose NH3+ as the start terminus at the first residue which is leucine
and COO- as my end terminus which is also on a leucine residue, which is
when it says it cant recognize atom type OXT on my last leucine residue.
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