[gmx-users] grompp: "invalid bond type" error

Olivia Waring owaring at princeton.edu
Tue Nov 1 22:32:05 CET 2011

Dear Gromacs users,

First of all, many thanks to Justin for his assistance with my previous

I have defined a new residue type in the oplsaa force field, changing the
aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try
to preprocess, I get the following output:

WARNING 1 [file ffbonded.itp, line 58]:
  Overriding Bond parameters.

  old: 0.1229 476976 0.1229 476976
  new: C     O      1    0.13270   179075.2

WARNING 2 [file ffbonded.itp, line 64]:
  Overriding Bond parameters.

  old: 0.1522 265266 0.1522 265266
  new: C    CT      1    0.14950   265265.6

WARNING 3 [file ffbonded.itp, line 67]:
  Overriding Bond parameters.

  old: 0.149 334720 0.149 334720
  new: CA    C      1    0.14240   392459.2

WARNING 4 [file ffbonded.itp, line 73]:
  Overriding Bond parameters.

  old: 0.1419 374050 0.1419 374050
  new: C    CB      1    0.14240   392459.2

Program grompp, VERSION 4.5.4
Source code file: topdirs.c, line: 76

Fatal error:
Invalid bond type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The error is rather cryptic, and I'm having trouble tracking it down... I
even went to the source code (topdirs.c), but I'm still not sure where
exactly this "invalid bond type" is being defined.

Thank you so much for your help,

Olivia Waring (王维娅)
Princeton University '12
AB Chemistry
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