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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