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
--
========================================
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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