Thank you so much for your quick reply! Below please find my topology file:
; Include forcefield parameters #include "hautklein.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein_chain_1 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 ALK rtp ALK q 0.0 1 CH3 0 ALK CH3 1 0 15.035 ; qtot 0 2 CH2 0 ALK CH2A 2 0 14.027 ; qtot 0 3 CH2 0 ALK CH2B 3 0 14.027 ; qtot 0 4 CH2 0 ALK CH2C 4 0 14.027 ; qtot 0 5 CH2 0 ALK CH2D 5 0 14.027 ; qtot 0 6 CH2 0 ALK CH2E 6 0 14.027 ; qtot 0 7 CH2 0 ALK CH2F 7 0 14.027 ; qtot 0 8 CH2 0 ALK CH2G 8 0 14.027 ; qtot 0 9 CH2 0 ALK CH2H 9 0 14.027 ; qtot 0 10 CH2 0 ALK CH2I 10 0 14.027 ; qtot 0 11 CH2 0 ALK CH2J 11 0 14.027 ; qtot 0 12 CH2 0 ALK CH2K 12 0 14.027 ; qtot 0 13 S 0 ALK S 13 0 32.06 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 2 3 1 3 4 1 4 5 1 5 6 1 6 7 1 7 8 1 8 9 1 9 10 1 10 11 1 11 12 1 12 13 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 2 5 1 3 6 1 4 7 1 5 8 1 6 9 1 7 10 1 8 11 1 9 12 1 10 13 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 2 3 4 1 3 4 5 1 4 5 6 1 5 6 7 1 6 7 8 1 7 8 9 1 8 9 10 1 9 10 11 1 10 11 12 1 11 12 13 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 3 2 3 4 5 3 3 4 5 6 3 4 5 6 7 3 5 6 7 8 3 6 7 8 9 3 7 8 9 10 3 8 9 10 11 3 9 10 11 12 3 10 11 12 13 3 [ constraints ] ; i j funct b0 1 2 1 0.0153 2 3 1 0.0153 3 4 1 0.0153 4 5 1 0.0153 5 6 1 0.0153 6 7 1 0.0153 7 8 1 0.0153 8 9 1 0.0153 9 10 1 0.0153 10 11 1 0.0153 11 12 1 0.0153 12 13 1 0.0182 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_1 1 Does this help? Thanks so much again, Olivia On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry
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