Hi,
Thanks for the resource! Do you really think the PATH is the problem? As you can see below- all the program elements (pdbfile and .sh script) are in the path I specified.
Macintosh:amber14 Me$ echo $AMBERHOME/Users/Me/amber14
Macintosh:amber14 Me$ pwd/Users/me/amber14
so I am in /Users/me/amber14
Macintosh:amber14 ChristopherGaughan$ ls -ltrtotal 36728--------------bunch of other stuff-------------------
drwxr-xr-x. 3 Me staff 102 Feb 6 17:19 VMD 1.9.2.app-rwxrwxrwx 1 Me staff 1635 Feb 6 22:55 vmd_box_dims.sh-rw-r--r-- 1 Me staff 2616225 Feb 6 22:55 amber_tut_DOPC.pdb
all seem to be in the path? No?
Does all this need to be done on the command line in VMD (which is .csh)? 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 - 10:00:03 PST
