Thank you Hannes!
I am undoubtedly a nube and even a simple shell script can throw me, please bear with my ignorance here
The shell script comes directly out of the tutorial for "An Amber Lipid Force Field...."
tried it on two systems, blacklight and my own:
/Users/Me/amber14Macintosh:amber14 Me$ export AMBERHOME=`pwd`Macintosh:amber14 Me$ vmd_box_dims.sh -i amber_tut_DOPC.pdb -s water-bash: vmd_box_dims.sh: command not found
I made sure to make the file executable.the pdb and shell script are in the same directory
The script has the shebang bash thing on the first line. I'm in a bash shell. I looked for the control-R thing on line 9, found an esac command.
From: "hannes.loeffler.stfc.ac.uk" <hannes.loeffler.stfc.ac.uk>
To: alpharecept.yahoo.com; amber.ambermd.org
Sent: Saturday, February 7, 2015 4:12 AM
Subject: RE: [AMBER] vmd_box_dims.sh
That's such a simple shell script that there is really not much to explain. The tutorial tells you to give the script a PDB file and a VMD selection (look into their manuals if you do not know how to make one of those). BTW, this script comes out of AMBER tutorial A16. Would have been good to mention that too.
It's a shell script so you will have to run it from the command line. I suggest to familiarise yourself with the shell and the command line because it is really so basic and you will probably need it very frequently.
When you say you can't get it to work, it would be really useful to mention what exactly you did and what the result was. I couldn't get it to run initially either because the script was apparently stored on some MSDOS-like system (and has a spurious Ctrl-R on line 9) and had to convert it first.
Cheers,
Hannes.
________________________________________
From: Chris Chris [alpharecept.yahoo.com]
Sent: 07 February 2015 04:18
To: AMBER Mailing List
Subject: [AMBER] vmd_box_dims.sh
Can someone tell me how to use vmd_box_dims.sh? I have installed amber 14 with AmberTools on my mac OSX and cannot get this script to work. Does it work in the command line on vmd? if not where do I put that script in the amber directories. I tried putting it in /Users/Me/amber14/AmberTools/src/etc/
The tutorial tells me the syntax and flags to use it but doesn't tell me how to use it
Sorry if this is a trivial question
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Received on Sat Feb 07 2015 - 08:30:02 PST
