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error when using fg2cg tool
- thu nguyen
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10 years 11 months ago #1647
by thu nguyen
error when using fg2cg tool was created by thu nguyen
Dear all,
I use tool fg2cg to convert CG to AA bead. But the error appear
Name of CG water in topology should be W
Segmentation fault (core dumped)
But i checked cg.top and CG water name was W, there is not mistake.
How i can fix this error ?
Thankful for any help!
Thu
I use tool fg2cg to convert CG to AA bead. But the error appear
Name of CG water in topology should be W
Segmentation fault (core dumped)
But i checked cg.top and CG water name was W, there is not mistake.
How i can fix this error ?
Thankful for any help!
Thu
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- djurre
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10 years 11 months ago #1648
by djurre
Replied by djurre on topic error when using fg2cg tool
Like this it is hard to say what the problem is. Maybe you can paste you top files and the command line you use here?
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- thu nguyen
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10 years 11 months ago #1649
by thu nguyen
Replied by thu nguyen on topic error when using fg2cg tool
I use the comamnd
g_fg2cg_331 -pfg system.top -pcg cg.top -n 0 -c cg.gro -o fg.gro
file cg.top
#include "martini_v2.2.itp"
#include "Protein_X.itp"
#define RUBBER_BANDS
#include "martini_v2.0_lipids.itp"
[ system ]
; name
Cg system
[ molecules ]
; name number
Protein_X 1
POPC 392
W 8792
g_fg2cg_331 -pfg system.top -pcg cg.top -n 0 -c cg.gro -o fg.gro
file cg.top
#include "martini_v2.2.itp"
#include "Protein_X.itp"
#define RUBBER_BANDS
#include "martini_v2.0_lipids.itp"
[ system ]
; name
Cg system
[ molecules ]
; name number
Protein_X 1
POPC 392
W 8792
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- xavier
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10 years 11 months ago #1651
by xavier
Replied by xavier on topic error when using fg2cg tool
The line defining the rubberband should be placed before the inclusion of the protein itp.
thu nguyen wrote: I use the comamnd
g_fg2cg_331 -pfg system.top -pcg cg.top -n 0 -c cg.gro -o fg.gro
file cg.top
#include "martini_v2.2.itp"
#include "Protein_X.itp"
#define RUBBER_BANDS
#include "martini_v2.0_lipids.itp"
[ system ]
; name
Cg system
[ molecules ]
; name number
Protein_X 1
POPC 392
W 8792
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- djurre
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10 years 11 months ago #1653
by djurre
Replied by djurre on topic error when using fg2cg tool
One thing that goes wrong is that you define "RUBBER_BANDS" after you include the protein itp file. This way there will be no elastic network defined on you protein.
But that should not give the error you mention. Two other options: Is the number of protein particles/lipids and waters the same in the top and gro file and could you also paste the fg "system.top" flie?
But that should not give the error you mention. Two other options: Is the number of protein particles/lipids and waters the same in the top and gro file and could you also paste the fg "system.top" flie?
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- thu nguyen
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10 years 11 months ago #1654
by thu nguyen
Replied by thu nguyen on topic error when using fg2cg tool
Thank for your post !
My fg topology is
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_X 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include POPC chain topology
#include "popc_53a6.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
fg system
[ molecules ]
; Compound #mols
Protein_chain_X 1
POPC 392
SOL 8792
My fg topology is
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_X 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include POPC chain topology
#include "popc_53a6.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
fg system
[ molecules ]
; Compound #mols
Protein_chain_X 1
POPC 392
SOL 8792
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- thu nguyen
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10 years 11 months ago #1655
by thu nguyen
Replied by thu nguyen on topic error when using fg2cg tool
the number of residues is the same in cg top and cg gro file.
and there is only top file for fg in input, i want to have fg gro in output :-)
and there is only top file for fg in input, i want to have fg gro in output :-)
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- djurre
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10 years 11 months ago #1658
by djurre
Replied by djurre on topic error when using fg2cg tool
Instead of including the normal spc.itp file, you have to include the special itp file for bundled water that is used for the reverse transformation (see the reverse transformation tutorial for this file, FG_W.itp). Also, instead of calling the water "SOL" you have to call it "FG_W". One FG_W corresponds to one CG water molecule and 4 atomistic molecules.
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- thu nguyen
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10 years 11 months ago #1661
by thu nguyen
Replied by thu nguyen on topic error when using fg2cg tool
Thank Djurre !
I created fg.gro but all of coordinate values is zero. What's wrong in my work ?
I created fg.gro but all of coordinate values is zero. What's wrong in my work ?
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10 years 11 months ago #1663
by xavier
Replied by xavier on topic error when using fg2cg tool
It is difficult to say from the information you gave.
I suggest you cleaned your files and start again from scratch and proceed step by step checking if things go well and at which point things go wrong. Once something goes wrong you try to understand why and report to the forum when you et a better idea of what is going wrong.
I suggest you cleaned your files and start again from scratch and proceed step by step checking if things go well and at which point things go wrong. Once something goes wrong you try to understand why and report to the forum when you et a better idea of what is going wrong.
thu nguyen wrote: Thank Djurre !
I created fg.gro but all of coordinate values is zero. What's wrong in my work ?
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