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 <[email protected]
<mailto:[email protected]>> 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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