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initram.sh dependecy error
- omkar73
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1 year 2 months ago #9575
by omkar73
initram.sh dependecy error was created by omkar73
I am following the backward mapping tutorial,
when I run the initram.sh command:
./initram.sh -f CG_posre.gro -o aa_charmm.gro -to charmm36 -p topol.top
I get this error:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram.sh -f CG_posre.gro -o aa_charmm.gro -to charmm36 -p topol.top
Checking dependencies:
backward.py ... /home/usha/work/gromacstut/martini3/BackwardMapping/aquaporine_backmap/backward.py
gmx ... /usr/local/gromacs/bin/gmx
grompp ... Missing dependency: grompp
How do I resolve this, thank you.
when I run the initram.sh command:
./initram.sh -f CG_posre.gro -o aa_charmm.gro -to charmm36 -p topol.top
I get this error:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram.sh -f CG_posre.gro -o aa_charmm.gro -to charmm36 -p topol.top
Checking dependencies:
backward.py ... /home/usha/work/gromacstut/martini3/BackwardMapping/aquaporine_backmap/backward.py
gmx ... /usr/local/gromacs/bin/gmx
grompp ... Missing dependency: grompp
How do I resolve this, thank you.
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- riccardo
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1 year 2 months ago #9576
by riccardo
Replied by riccardo on topic initram.sh dependecy error
Seems that initram can't find GROMACS. Do you have GROMACS installed ?
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- omkar73
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1 year 2 months ago #9577
by omkar73
Replied by omkar73 on topic initram.sh dependecy error
Yes I have it installed
gmx -h:
:-) GROMACS - gmx, 2022.4 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/usha/work/gromacstut/martini3/BackwardMapping/aquaporine_backmap
Command line:
gmx -h
SYNOPSIS
gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
[-[no]backup]
OPTIONS
Other options:
-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (no)
Print copyright information on startup
-nice <int> (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files exist
Additional help is available on the following topics:
commands List of available commands
selections Selection syntax and usage
To access the help, use 'gmx help <topic>'.
For help on a command, use 'gmx help <command>'.
GROMACS reminds you: "Humans are allergic to change. They love to say, 'We've always done it this way.' I try to fight that. That's why I have a clock on my wall that runs counter-clockwise." (Grace Hopper)
gmx -h:
:-) GROMACS - gmx, 2022.4 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/usha/work/gromacstut/martini3/BackwardMapping/aquaporine_backmap
Command line:
gmx -h
SYNOPSIS
gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
[-[no]backup]
OPTIONS
Other options:
-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (no)
Print copyright information on startup
-nice <int> (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files exist
Additional help is available on the following topics:
commands List of available commands
selections Selection syntax and usage
To access the help, use 'gmx help <topic>'.
For help on a command, use 'gmx help <command>'.
GROMACS reminds you: "Humans are allergic to change. They love to say, 'We've always done it this way.' I try to fight that. That's why I have a clock on my wall that runs counter-clockwise." (Grace Hopper)
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- riccardo
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1 year 2 months ago #9578
by riccardo
Replied by riccardo on topic initram.sh dependecy error
Maybe then it's because initram is looking for gromacs < 5. Are you using the github version of backward?
github.com/tsjerk/backward
If not, try that one.
If not, try that one.
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