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

[Olivia Waring]

Dear Gromacs users,

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

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


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