[gmx-users] Atom OT1 in the residue

[Мижээ Батсайхан]

Dear Justin,

Thank you very much your help.

Best regards,

Miji

> ------------------------------
>
> Message: 2
> Date: Tue, 23 Jan 2018 06:44:59 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Atom OT1 in the residue
> Message-ID: <82fdffdd-85b4-56ab-8445-27f6ca0aa5a5 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/23/18 1:59 AM, ????? ????????? 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
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