RE: AMBER: sander problem

From: Ross Walker <>
Date: Thu, 16 Feb 2006 13:20:45 -0800

Dear Brian,


> I am going through the tutorial for Amber
> (
> _one/section5.htm)
> and have come across a command that Amber is not
> finding. The command is process_mdout.perl
> Below is an excerpt from the tutorial:
> mkdir polyAT_gb_md1_12Acut
> mkdir polyAT_gb_md1_nocut
> cd polyAT_gb_md1_12Acut
> process_mdout.perl ../polyAT_gb_md1_12Acut.out
> cd ../polyAT_gb_md1_nocut
> process_mdout.perl ../polyAT_gb_md1_nocut.out

My apologies for this, the tutorials were written as part of a workshop I
hosted and there the machines were setup to have that script in their path.
The script is not part of the amber software but is a simple perl script I
provide for easily processing sander output files. If you go to the main DNA
tutorial on the amber site you will find a version that wasn't written for
the workshop:

Section 2 contains a link to the perl script:

I will also add a link to the script in the workshop tutorial so people can
download the script.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Sun Feb 19 2006 - 06:10:18 PST
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