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Error when grompp
- Leliel
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10 years 9 months ago #1832
by Leliel
Error when grompp was created by Leliel
Hi,
i am using martini FF to build a coarse grained DNA model,and i have made the gro itp top file artificially.
when i use the grompp command to do a em.mdp process,there lies a fatal error says
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule.
i write this itp file referring martini_v2.0_lipid.itp , and i change the molecule name.but i cant figure out which part goes wrong??
can you help?
Thanks in advance!!
i am using martini FF to build a coarse grained DNA model,and i have made the gro itp top file artificially.
when i use the grompp command to do a em.mdp process,there lies a fatal error says
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule.
i write this itp file referring martini_v2.0_lipid.itp , and i change the molecule name.but i cant figure out which part goes wrong??
can you help?
Thanks in advance!!
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- djurre
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10 years 9 months ago #1833
by djurre
Replied by djurre on topic Error when grompp
As far as I know there is currently no working Martini model DNA, so I'm affraid we can't help you with this.
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- Clement
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10 years 9 months ago #1834
by Clement
Replied by Clement on topic Error when grompp
Could you copy/paste here the itp/top files you built? If not too long of course... But shouldn't be.
Just a comment: problems with building itp/top files are more related to the GROMACS mailing list... We can help here on the Martini-specific problems (extension of the existing set of compounds available, development of new models), but the "philosophy" and the reasoning behind the various file formats/the functioning of GROMACS itself is something you'll find on the GROMACS website.
Just a comment: problems with building itp/top files are more related to the GROMACS mailing list... We can help here on the Martini-specific problems (extension of the existing set of compounds available, development of new models), but the "philosophy" and the reasoning behind the various file formats/the functioning of GROMACS itself is something you'll find on the GROMACS website.
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- Leliel
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10 years 9 months ago #1835
by Leliel
Replied by Leliel on topic Error when grompp
Hi,
i have compared your Martini's itp/top files with the fine-grained ones,but there are some differences... so i am confused.
my files are:
top:
;INCLUDE FORCE FIELD PARAMETERS
#include "martini_v2.2.itp"
#include "martini_v1.0_DNA.itp"
[ system ]
;NAME
DUPLEX 3U2N CG MODELING
[ molecules ]
;COMPOUND #MOL
DNA 1
while my itp file for DNA are:
[moleculetype]
;molname nrexcl
DNA 1
[atom]
;id type resnr residu atom cgnr charge
1 Qa 1 1DC PO1 1 -1.0
2 C1 1 1DC CC1 2 0
....
[bonds]
; i j funct length force.c
1 2 1 0.47 1250
2 3 1 0.47 1250
....
[angles]
; i j k funct angle force.c
1 2 3 2 120 25
1 2 4 2 120 25
....
the mistakes are in the line110, the first line below [bonds] section
thanks in advance!
i have compared your Martini's itp/top files with the fine-grained ones,but there are some differences... so i am confused.
my files are:
top:
;INCLUDE FORCE FIELD PARAMETERS
#include "martini_v2.2.itp"
#include "martini_v1.0_DNA.itp"
[ system ]
;NAME
DUPLEX 3U2N CG MODELING
[ molecules ]
;COMPOUND #MOL
DNA 1
while my itp file for DNA are:
[moleculetype]
;molname nrexcl
DNA 1
[atom]
;id type resnr residu atom cgnr charge
1 Qa 1 1DC PO1 1 -1.0
2 C1 1 1DC CC1 2 0
....
[bonds]
; i j funct length force.c
1 2 1 0.47 1250
2 3 1 0.47 1250
....
[angles]
; i j k funct angle force.c
1 2 3 2 120 25
1 2 4 2 120 25
....
the mistakes are in the line110, the first line below [bonds] section
thanks in advance!
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- Clement
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10 years 9 months ago #1836
by Clement
Replied by Clement on topic Error when grompp
"[atomS]", not "[atom]"
grompp doesn't find any atom defined, therefore complains there's no bonds to define...
grompp doesn't find any atom defined, therefore complains there's no bonds to define...
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