- Posts: 70
Error "Incorrect number of parameters - found 1, "
- djpittdj
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Topic Author
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9 years 7 months ago #4063
by djpittdj
Error "Incorrect number of parameters - found 1, " was created by djpittdj
Dear all:
I'm trying to run a simulation on a protein with multiple chains.
I was able to generate the CG topology and coordinates but during run preparation using grompp, I encountered the problem:
"Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond."
I'm using martinize.py version 2.4, martini_v2.2.itp and Gromacs 4.6.6. For the mdp file, I used the one provided in the tutorial: " md.chem.rug.nl/cgmartini/images/stories/...imization-vaccum.mdp "
Commands that I've used:
1. ./martinize.py -cys auto \
-f prot.pdb \
-o prot.CG.top \
-x prot.CG.pdb \
-dssp /scratch/local/bin/dssp \
-p backbone \
-pf 1000 \
-ff martini22
2. grompp -f minim-vacuum.mdp \
-c prot.CG.pdb \
-p prot.CG.top \
-o minim-vacuum
the topology file is like:
####
#include "martini_v2.2.itp"
#include "Protein_A.itp"
#include "Protein_C.itp"
#include "Protein_B.itp"
#include "Protein_D.itp"
[ system ]
; name
Martini system
[ molecules ]
; name number
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
####
This page ( www.gromacs.org/Documentation/Errors ) suggests that the topology file might be messed up but the only thing that I do is to change "martini.itp" in the topology file marininize.py generates into "martini_v2.2.itp".
Anyone has any idea about this?
Thank you very much.
Jian
I'm trying to run a simulation on a protein with multiple chains.
I was able to generate the CG topology and coordinates but during run preparation using grompp, I encountered the problem:
"Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond."
I'm using martinize.py version 2.4, martini_v2.2.itp and Gromacs 4.6.6. For the mdp file, I used the one provided in the tutorial: " md.chem.rug.nl/cgmartini/images/stories/...imization-vaccum.mdp "
Commands that I've used:
1. ./martinize.py -cys auto \
-f prot.pdb \
-o prot.CG.top \
-x prot.CG.pdb \
-dssp /scratch/local/bin/dssp \
-p backbone \
-pf 1000 \
-ff martini22
2. grompp -f minim-vacuum.mdp \
-c prot.CG.pdb \
-p prot.CG.top \
-o minim-vacuum
the topology file is like:
####
#include "martini_v2.2.itp"
#include "Protein_A.itp"
#include "Protein_C.itp"
#include "Protein_B.itp"
#include "Protein_D.itp"
[ system ]
; name
Martini system
[ molecules ]
; name number
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
####
This page ( www.gromacs.org/Documentation/Errors ) suggests that the topology file might be messed up but the only thing that I do is to change "martini.itp" in the topology file marininize.py generates into "martini_v2.2.itp".
Anyone has any idea about this?
Thank you very much.
Jian
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- jaakko
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9 years 7 months ago #4064
by jaakko
Replied by jaakko on topic Error "Incorrect number of parameters - found 1, "
Hi,
you should check your itp file for lines just after [ bonds ]. Sounds like there's either a line with incorrect parameters or more likely a line that doesn't describe a bond but grompp thinks it does.
- Jaakko
you should check your itp file for lines just after [ bonds ]. Sounds like there's either a line with incorrect parameters or more likely a line that doesn't describe a bond but grompp thinks it does.
- Jaakko
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- djpittdj
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Topic Author
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9 years 7 months ago #4065
by djpittdj
Replied by djpittdj on topic Error "Incorrect number of parameters - found 1, "
Right, I found that the output generated by Martinize.py lacks force constant for cys-cys bond, after adding 2500 force constant to the line of cys-cys bond, it works OK. Thanks.
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- djpittdj
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Topic Author
- Visitor
9 years 7 months ago #4067
by djpittdj
Replied by djpittdj on topic Error "Incorrect number of parameters - found 1, "
In line 1312 of Marinize.py version 2.4, there's no force constant for the disulfide bond, is it a bug or it's what's supposed to be?
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- xavier
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- Posts: 416
9 years 7 months ago #4068
by xavier
Replied by xavier on topic Error "Incorrect number of parameters - found 1, "
If there is no force constant in your itp it might be an imperfection of martinize.
You can always add it by hand in your itp file. We normally use a 10000 kJ/mol/nm^2
You can always add it by hand in your itp file. We normally use a 10000 kJ/mol/nm^2
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- sumar
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- Visitor
8 years 2 months ago #5368
by sumar
Replied by sumar on topic Error "Incorrect number of parameters - found 1, "
Hello..
I have same problem (Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond). But I after I read this, I still did'nt understand.
Could you explain to me, what kind of line that I have to changes??
this is My .itp file after bonds :
[ bonds ]
; Backbone bonds
29 30 1 0.35000 1250 ; GLY(C)-GLY(C)
30 31 1 0.35000 1250 ; GLY(C)-CYS(C)
31 33 1 0.35000 1250 ; CYS(C)-GLY(C)
33 34 1 0.35000 1250 ; GLY(C)-GLY(C)
64 67 1 0.35000 1250 ; ARG(C)-MET(C)
95 96 1 0.35000 1250 ; GLY(C)-GLY(C)
96 97 1 0.35000 1250 ; GLY(C)-CYS(C)
97 99 1 0.35000 1250 ; CYS(C)-GLY(C)
99 100 1 0.35000 1250 ; GLY(C)-GLY(C)
cheers
Sumar
I have same problem (Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond). But I after I read this, I still did'nt understand.
Could you explain to me, what kind of line that I have to changes??
this is My .itp file after bonds :
[ bonds ]
; Backbone bonds
29 30 1 0.35000 1250 ; GLY(C)-GLY(C)
30 31 1 0.35000 1250 ; GLY(C)-CYS(C)
31 33 1 0.35000 1250 ; CYS(C)-GLY(C)
33 34 1 0.35000 1250 ; GLY(C)-GLY(C)
64 67 1 0.35000 1250 ; ARG(C)-MET(C)
95 96 1 0.35000 1250 ; GLY(C)-GLY(C)
96 97 1 0.35000 1250 ; GLY(C)-CYS(C)
97 99 1 0.35000 1250 ; CYS(C)-GLY(C)
99 100 1 0.35000 1250 ; GLY(C)-GLY(C)
cheers
Sumar
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- sumar
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- Visitor
8 years 2 months ago #5369
by sumar
Hello..
I have same problem (Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond). But I after I read this, I still did'nt understand.
Could you explain to me, what kind of line that I have to changes??
this is My .itp file after bonds :
[ bonds ]
; Backbone bonds
29 30 1 0.35000 1250 ; GLY(C)-GLY(C)
30 31 1 0.35000 1250 ; GLY(C)-CYS(C)
31 33 1 0.35000 1250 ; CYS(C)-GLY(C)
33 34 1 0.35000 1250 ; GLY(C)-GLY(C)
64 67 1 0.35000 1250 ; ARG(C)-MET(C)
95 96 1 0.35000 1250 ; GLY(C)-GLY(C)
96 97 1 0.35000 1250 ; GLY(C)-CYS(C)
97 99 1 0.35000 1250 ; CYS(C)-GLY(C)
99 100 1 0.35000 1250 ; GLY(C)-GLY(C)
cheers
Replied by sumar on topic Error "Incorrect number of parameters - found 1, "
jaakko wrote: Hi,
you should check your itp file for lines just after [ bonds ]. Sounds like there's either a line with incorrect parameters or more likely a line that doesn't describe a bond but grompp thinks it does.
- Jaakko
Hello..
I have same problem (Fatal error: Incorrect number of parameters - found 1, expected 2 or 4 for Bond). But I after I read this, I still did'nt understand.
Could you explain to me, what kind of line that I have to changes??
this is My .itp file after bonds :
[ bonds ]
; Backbone bonds
29 30 1 0.35000 1250 ; GLY(C)-GLY(C)
30 31 1 0.35000 1250 ; GLY(C)-CYS(C)
31 33 1 0.35000 1250 ; CYS(C)-GLY(C)
33 34 1 0.35000 1250 ; GLY(C)-GLY(C)
64 67 1 0.35000 1250 ; ARG(C)-MET(C)
95 96 1 0.35000 1250 ; GLY(C)-GLY(C)
96 97 1 0.35000 1250 ; GLY(C)-CYS(C)
97 99 1 0.35000 1250 ; CYS(C)-GLY(C)
99 100 1 0.35000 1250 ; GLY(C)-GLY(C)
cheers
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