[gmx-users] How to avoid generating wrong dihedrals?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 1 08:35:59 CEST 2009

Hi Chaofu Wu,

Indeed it seems improper to have a dihedral with C-N-H-H. So it's an
improper dihedral! :p
The problem might arise from the addition of hydrogens. Could you give
more information? Which force field did you use? what residue was
causing the problem? Can you reproduce the problem starting only with
that residue (and then paste it, so that one of us might reproduce



2009/7/1 wuxiao <xiaowu759 at hotmail.com>:
> Dear gmx users,
>   I try to generate gro and top files using pdb2gmx, and this procedure
> finishs without any error. However, when I run grompp from these files, many
> errors are encountered such as:
>   ......
>   ERROR 124 [file g04.top, line 20027]
>   No default Ryckaert-Bell. types
>   ......
>   I gusess it is dihedrals that cause these errors. So I look for the line
> 20027 in the file g04.top. only to find that these dihedrals are C-N-H-H,
> obviously wrong. How to avoid these errors? Could you give me some help to
> cope with them? Thank you for attention.
> Sincerely,
> Chaofu Wu
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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