Hi Victor,
It is best if such questions go to the amber mailing list so that others can
benefit from the answers and so any answers get archived to
http://amber.ch.
ic.ac.uk/archive/ so I am copying this reply here.
The issue is one of whether the process_mdout.pl file is in a directory in
your path. I assume you have downloaded the perl script, if not you can get
it here:
http://amber.scripps.edu/tutorials/basic/tutorial1/files/process_mdout.perl.
As of amber9 this script is included in the tools directory.
I typically place this in /usr/local/bin which is in my path so simply
specifying the file will work.
However, if you place it in a directory that is not specified in your path
(and you don't have "./" in your path then you need to execute it with)
./process_mdout.pl blah1 blah2 blah3
or specify the full path to the file if it is in a different directory to
the one you are currently in.
E.g.
/home/user_dir/process_mdout.pl blah1 blah2 blah3...
It is possible that you receive the error:
Permission denied. In this case you have to tell the operating system that
the file is executable which you can do with:
chmod +x process_mdout.pl (assuming you own the file).
I hope this helps
All the best
Ross
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| San Diego Supercomputer Center |
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From: Prof.Dr.rer.nat.Dipl.-Ing.BS. [mailto:victorbres3tw.yahoo.com.tw]
Sent: Friday, June 01, 2007 05:34
To: amber_tutorial_query.rosswalker.co.uk
Subject: process_mdout.perl
2020, Jun 01(Fr), 2007
Hi, dear Prof. Ross Walker,
I have made sofar (Amber 8.0) to the bottom of Page 5 von 13 of your
Tutorial B1 - Section 3.
mkdir polyAT_vac_md1_12Acut
cd polyAT_vac_md1_12Acut
process_mdout.perl ../polyAT_vac_md1_12Acut.out
But:
bash: process_mdout: command not found
why?
The reason may be:
"process_mdout.perl" is a text file, not an execution file.
Thank you very much!
Victor
Dr.rer.nat.Dipl.-Ing.B.S. Victor Wei-Keh Wu,
1. Dept. of Chemical and Material Engineering, National Kaohsiung Univ. of
Applied Sciences, 80782 Kao-Hsiung, Taiwan.
Mo-We: Fax:+886-(0)7-3830674, Tel:-3814526-ext-5119
2. Victor Basic Research Laboratory e.V., D-33602 Bielefeld, Germany
http:// <
http://www.che.kuas.edu.tw/> www.che.kuas.edu.tw
<
http://www.che.kuas.edu.tw/> ,
Email: victorbres3tw.yahoo.com.tw, Tel:+886-(0)919-300-525(24hr, direct),
-(0)2-2932-5975(H)
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Received on Sun Jun 03 2007 - 06:07:41 PDT
