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

[Mark Abraham]

On 2/11/2011 8:32 AM, 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]:

You'll need to inspect at and before this line in this file to diagnose.

Mark

>   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 (???)
> Princeton University '12
> AB Chemistry
>
>
>

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