[gmx-users] Atom OT1 in the residue

[Justin Lemkul]

On 1/23/18 1:59 AM, Мижээ Батсайхан wrote:
> Dear gmx user,
>
> I am using gromacs 5.1 with charmm36-march2017 force field. I have an error
> as following:
>
> "Atom OT1 in residue DTRP 4 was not found in rtp entry DTRP with 24 atoms
> while sorting atoms."
>
> How can I fix this error?
>
> Additionally, I modified the structure of last DTRP residue from the TRP
> residue. I guess that there is no structural problem.
>

The D-amino acids are not in residuetypes.dat, so you probably have a 
false chain termination and the patching gets screwed up. See step 5 in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

This holds true for anything non-standard. We've made the error message 
clearer in the latest release.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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