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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