[gmx-users] grompp: "invalid bond type" error
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 2 00:13:57 CET 2011
Olivia Waring wrote:
> Thank you so much for your quick reply!
>
> Below please find my topology file:
>
>
> ; Include forcefield parameters
> #include "hautklein.ff/forcefield.itp"
>
The problems you are experiencing are probably coming from this file, or perhaps
somewhere else in your custom force field. The error suggests that your
[defaults] directive is improperly constructed.
-Justin
> [ 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 <jalemkul at vt.edu
> <mailto:jalemkul at 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 <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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>
>
> --
> Olivia Waring (王维娅)
> Princeton University '12
> AB Chemistry
>
--
========================================
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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