normal problem encounterd when I used cg_bonds.tcl

  • Jinyoung
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2 years 10 months ago - 2 years 10 months ago #9108 by Jinyoung
Hi,
I tried to visualize the MARTINI force field system with VMD by using cg_bonds.tcl

When I used cg_bonds.tcl,
vmd > cg_bonds -top system.top
key "na" not known in dictionary
vmd > cg_bonds -tpr ../PROD/prod_1.tpr
couldn't execute "/usr/bin/gmxdump": no such file or directory

But before I prompt VMD, I source gromacs as below:
source ~/apps/GROMACS/gromacs-2020.4_gcc-7.5.0_openmpi-4.0.2/bin/GMXRC

how can I solve this problem?

Best regards

Jinyoung
Last edit: 2 years 10 months ago by Jinyoung.

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2 years 10 months ago #9112 by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
This is a problem pf cg_bonds with newer Gromacs version. cg_bonds is looking for "gmxdump" which was renamed in recent Gromacs version.

Try using the following:
cg_bonds [b]-gmx /usr/local/gromacs/bin/gmx[/b] -tpr ...

*NOTE* that your path to "gmx" might be different! Look for where Gromacs is installed and where that "gmx" file is.

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2 years 9 months ago #9156 by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below

child process exited abnormally

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2 years 9 months ago #9157 by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below

child process exited abnormally

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2 years 9 months ago #9158 by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below

child process exited abnormally

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2 years 9 months ago #9166 by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below

child process exited abnormally

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2 years 7 months ago #9254 by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
It would be useful if you specified the command you used.

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