[gmx-users] Atom was not found

Monoj Mon Kalita mon.123chem at gmail.com
Thu Jun 19 04:37:38 CEST 2014

If your protein is an oligomer, then you can check the termini of the
monomers. After doing the pdb2gmx sometime GROMACS removes those 'TER'
words at end of each monomers, so what you can do is retype 'TER' at the
end of each monomers. This might help you.

> Message: 1
> Date: Wed, 18 Jun 2014 10:30:14 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Atom was not found
> Message-ID: <53A1A276.7030800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> On 6/18/14, 9:21 AM, h.alizadeh at znu.ac.ir wrote:
> Dear Users,
> I want to simulate a protein by GROMACS.
> When I use pdb2gmx command, topology and other files are produced from my
> pdb file.
> But when I define a box for my protein by editconf before pdb2gmx, I face
> with this fatal error:
> "Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms
> while sorting atoms"
> of course as I said, without defining a box, pdb2gmx is ok!!
> Defining the box alone should have no effect on what the atoms are, unless
> something has been renamed by changing formats or something.  Do a diff
> the files before and after editconf, but there is no real reason why
> should
> have been changed, or any real reason to manipulate the box before

> -Justin

 With Regards
Monoj Mon Kalita
 Taipei, Taiwan

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