[gmx-users] atom type OXT

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Sep 9 14:50:16 CEST 2011

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  

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).


> 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


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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