[gmx-users] Re: atom type OXT

Sweta Iyer iyer at wehi.EDU.AU
Wed Sep 7 08:11:00 CEST 2011

> 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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