[gmx-users] Adding a new residue and Duplicate atom index () in angles error

[Mijiddorj B]

Dear Justin,

Thank you very much for your prompt response.
Do you mean that I made a mistake when I define the bonds in .rtp file?

Best regards,
Mijiddorj



> ------------------------------
>
> Message: 6
> Date: Thu, 3 Oct 2019 15:47:13 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Adding a new residue and Duplicate atom index
>         () in angles error
> Message-ID: <42335958-7fdd-1862-22a9-9b590d1ce6ed at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/3/19 11:56 AM, Mijiddorj B wrote:
> > Dear GMX experts,
> >
> > I am trying to prepare CHARMM36 parameter for non-standard amino acid
> using
> > some instructions  such as
> >
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> > and
> > the user manual.
> >
> > After I modified merged.rtp, merged.hdb, and residuetype.data files,
> > gmxpdb2gmx successfully created
> > gro, topol, and posre files.
> >
> > However, gmx grompp could not generate the tpr file because of several -
> > maxwarn.
> >
> > The warmings commented as"duplicate atom index (34) in angles" and
> > "duplicate atom index (34) in dihedrals".
> >
> > I think this kind error is related to the topology file especially I need
> > to change ffbonded.itp of charmm36. However, I have no idea how to change
> > this file. Could you explain to me how to fix this problem?
>
> You have the same atom used twice in angle and dihedral interactions.
> This suggests an error in your .rtp entry, probably a typo, in which the
> same atom appears twice in angle and dihedral definitions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
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>
> ==================================================
>
>
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> End of gromacs.org_gmx-users Digest, Vol 186, Issue 5
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