AMBER Archive (2006)

Subject: RE: AMBER: sander problem

From: Brian Stupi (
Date: Thu Feb 16 2006 - 14:44:11 CST

Hello Amber community,

I am going through the tutorial for Amber
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

The computer error is as follows:

~/amber8/polyAT_gb_md1_nocut$ process_mdout.perl
-bash: process_mdout.perl: command not found

I ran the bugfix.all so Amber should be OK. If anyone
has a suggestion please let me know. Thank you in


Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to