[gmx-users] grompp: "invalid bond type" error
Olivia Waring
owaring at princeton.edu
Tue Nov 1 23:00:35 CET 2011
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 <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 | (540) 231-9080
> 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
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