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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
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