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

[Justin A. Lemkul]

Olivia Waring wrote:
> 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
> 

These four warnings suggest you're using values for bonded parameters that 
conflict with those present in the force field.  If you have reason to do this, 
then there's no problem, per se.  But be aware that you're using parameters the 
force field does not expect.

> 
> -------------------------------------------------------
> 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. 
> 

This error suggests a more fundamental problem in your topology, but without 
seeing the topology, there's little more that can be said.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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