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molmaker - dihedral type error
- Bjiarne
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10 years 10 months ago #1742
by Bjiarne
molmaker - dihedral type error was created by Bjiarne
Dear all,
I tried to create a gro-file for the surfactant C12E5 using the martini_v2.2P.itp forcefield and an itp-file for C12E5 build out of the file martini_v2.0_surfactants.itp
I get following error in the pp.log - file
Program grompp, VERSION 4.5.5
Source code file: topdirs.c, line: 128
Fatal error:
Invalid dihedral type 150
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I tried to identify the cause of the error by investigation of the used itp-files but I could not find anything. Does anyone has a suggestion what I can do?
With SDS the molmaker tool worked without any problems.
Thank you in advanced for any help.
I tried to create a gro-file for the surfactant C12E5 using the martini_v2.2P.itp forcefield and an itp-file for C12E5 build out of the file martini_v2.0_surfactants.itp
I get following error in the pp.log - file
Program grompp, VERSION 4.5.5
Source code file: topdirs.c, line: 128
Fatal error:
Invalid dihedral type 150
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I tried to identify the cause of the error by investigation of the used itp-files but I could not find anything. Does anyone has a suggestion what I can do?
With SDS the molmaker tool worked without any problems.
Thank you in advanced for any help.
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- jaakko
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10 years 10 months ago #1743
by jaakko
Replied by jaakko on topic molmaker - dihedral type error
Hi Bjiarne,
could you copy the exact command you used and check&tell what you did for the martini_v2.0_surfactants.itp file? I tried running molmaker with the same molecule and files without problems. Based on the error message it could be reading some angles with 150 default angle from later molecules to be part of dihedral definitions but if you have a clean itp for c12e5 there shouldn't be anything afterwards there...
- Jaakko
could you copy the exact command you used and check&tell what you did for the martini_v2.0_surfactants.itp file? I tried running molmaker with the same molecule and files without problems. Based on the error message it could be reading some angles with 150 default angle from later molecules to be part of dihedral definitions but if you have a clean itp for c12e5 there shouldn't be anything afterwards there...
- Jaakko
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- Bjiarne
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10 years 10 months ago #1744
by Bjiarne
Replied by Bjiarne on topic molmaker - dihedral type error
Hi jaakko,
Thank you for your fast reply. As well I am of the opinion, that something is wrong with my itp-file for C12E5, because it works with SDS.
The command I used:
./molmaker.py -ff martini_v2.2P.itp -i martini_v2.0_C12E5.itp -o molmaker_C12E5.gro
The itp-file for C12E5:
;;;;;; TOPOLOGIES FOR SURFACTANTS
;;;;;; C12E5
[moleculetype]
;name exclusions
EO5 1
[atoms]
1 SP2 1 EO5 OH 1 0.000 ;
2 SNa 1 EO5 O1 2 0.000 ;
3 SNa 1 EO5 O1 3 0.000 ;
4 SNa 1 EO5 O1 4 0.000 ;
5 SNa 1 EO5 O1 5 0.000 ;
6 SNa 1 EO5 O1 6 0.000 ;
7 C1 1 EO5 C1 7 0.000 ;
8 C1 1 EO5 C2 8 0.000 ;
9 C1 1 EO5 C3 9 0.000 ;
[ bonds ]
1 2 1 0.330 17000 ;
2 3 1 0.330 17000 ;
3 4 1 0.330 17000 ;
4 5 1 0.330 17000 ;
5 6 1 0.330 17000 ;
6 7 1 0.370 1250 ;
7 8 1 0.470 1250 ;
8 9 1 0.470 1250 ;
[angles]
1 2 3 1 130.00 50 ;
2 3 4 1 130.00 50 ;
3 4 5 1 130.00 50 ;
4 5 6 1 130.00 50 ;
5 6 7 2 120.00 25 ;
6 7 8 2 180.00 25 ;
7 8 9 2 180.00 25 ;
[dihedrals]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
2 3 4 5 1 180.00 1.96 1
2 3 4 5 1 0 0.18 2
2 3 4 5 1 0 0.33 3
2 3 4 5 1 0 0.12 4
3 4 5 6 1 180.00 1.96 1
3 4 5 6 1 0 0.18 2
3 4 5 6 1 0 0.33 3
3 4 5 6 1 0 0.12 4
1 2 4 2 150 50
3 2 4 2 140 50
5 4 2 2 70 100
6 4 2 2 50 25
4 7 8 2 180 11
7 8 9 2 180 76.6
2 4 7 2 149.7 169.2
[ dihedrals ]
; i j k l funct angle forcec. multiplic.
1 2 4 5 1 110 8 1
1 2 4 6 1 -20 5 1
3 2 4 5 1 -80 5 1
Thank you for your fast reply. As well I am of the opinion, that something is wrong with my itp-file for C12E5, because it works with SDS.
The command I used:
./molmaker.py -ff martini_v2.2P.itp -i martini_v2.0_C12E5.itp -o molmaker_C12E5.gro
The itp-file for C12E5:
;;;;;; TOPOLOGIES FOR SURFACTANTS
;;;;;; C12E5
[moleculetype]
;name exclusions
EO5 1
[atoms]
1 SP2 1 EO5 OH 1 0.000 ;
2 SNa 1 EO5 O1 2 0.000 ;
3 SNa 1 EO5 O1 3 0.000 ;
4 SNa 1 EO5 O1 4 0.000 ;
5 SNa 1 EO5 O1 5 0.000 ;
6 SNa 1 EO5 O1 6 0.000 ;
7 C1 1 EO5 C1 7 0.000 ;
8 C1 1 EO5 C2 8 0.000 ;
9 C1 1 EO5 C3 9 0.000 ;
[ bonds ]
1 2 1 0.330 17000 ;
2 3 1 0.330 17000 ;
3 4 1 0.330 17000 ;
4 5 1 0.330 17000 ;
5 6 1 0.330 17000 ;
6 7 1 0.370 1250 ;
7 8 1 0.470 1250 ;
8 9 1 0.470 1250 ;
[angles]
1 2 3 1 130.00 50 ;
2 3 4 1 130.00 50 ;
3 4 5 1 130.00 50 ;
4 5 6 1 130.00 50 ;
5 6 7 2 120.00 25 ;
6 7 8 2 180.00 25 ;
7 8 9 2 180.00 25 ;
[dihedrals]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
2 3 4 5 1 180.00 1.96 1
2 3 4 5 1 0 0.18 2
2 3 4 5 1 0 0.33 3
2 3 4 5 1 0 0.12 4
3 4 5 6 1 180.00 1.96 1
3 4 5 6 1 0 0.18 2
3 4 5 6 1 0 0.33 3
3 4 5 6 1 0 0.12 4
1 2 4 2 150 50
3 2 4 2 140 50
5 4 2 2 70 100
6 4 2 2 50 25
4 7 8 2 180 11
7 8 9 2 180 76.6
2 4 7 2 149.7 169.2
[ dihedrals ]
; i j k l funct angle forcec. multiplic.
1 2 4 5 1 110 8 1
1 2 4 6 1 -20 5 1
3 2 4 5 1 -80 5 1
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- jaakko
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10 years 10 months ago #1745
by jaakko
Replied by jaakko on topic molmaker - dihedral type error
Hi Bjiarne,
looks like my guess was right. If you look at the end of your itp file you've left some angles and dihedrals from the DDM itp there. Lines starting from: " 1 2 4 2 150 50" should be removed, check from the original surfactant itp file to see what went wrong.
- Jaakko
looks like my guess was right. If you look at the end of your itp file you've left some angles and dihedrals from the DDM itp there. Lines starting from: " 1 2 4 2 150 50" should be removed, check from the original surfactant itp file to see what went wrong.
- Jaakko
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- Bjiarne
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10 years 10 months ago #1746
by Bjiarne
Replied by Bjiarne on topic molmaker - dihedral type error
Hi Jaakko,
Thank you very much. Now it worked.
Best regards
Thank you very much. Now it worked.
Best regards
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