AMBER: RE: process_mdout.perl

From: Ross Walker <>
Date: Fri, 1 Jun 2007 12:47:04 -0700

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 so I am copying this reply here.
The issue is one of whether the file is in a directory in
your path. I assume you have downloaded the perl script, if not you can get
it here:

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)
./ 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.
/home/user_dir/ 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 (assuming you own the file).
I hope this helps
All the best

|\oss Walker

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From: Prof.Dr.rer.nat.Dipl.-Ing.BS. []
Sent: Friday, June 01, 2007 05:34
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
bash: process_mdout: command not found
The reason may be:
"process_mdout.perl" is a text file, not an execution file.
Thank you very much!

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:// <>
<> ,
Email:, Tel:+886-(0)919-300-525(24hr, direct),

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Received on Sun Jun 03 2007 - 06:07:41 PDT
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