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

[Mijiddorj B]

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?

Best regards