AMBER Archive (2006)

Subject: RE: AMBER: process_mdout.perl error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 19 2006 - 09:43:25 CDT

> I tried to follows the tutorial one, I found the error
> message when I tried
> to run process_mdout.perl. What should I do to solve this
> problem? Please
> kindly help, many thanks in advanced!
>
> [path]$ process_mdout.perl ../polyAT_vac_md1_12Acut.out
> bash: process_mdout.perl: command not found

Assuming you downloaded the perl script try:

perl process_mdout.perl ../polyAT_vac_md1_12Acut.out

As for xmgr you need to download and install it and then add it to your
path. See if you have xmgrace already installed on your machine. You can
find a redhat rpm here:
http://amber.ch.ic.ac.uk/tutorial/polyA-polyT_New/misc_files/xmgr-semistatic
-4.1.2-12.i386.rpm (I can't remember what redhat version this is for but it
is semi-static so may work). The main webpage is here:
http://plasma-gate.weizmann.ac.il/Xmgr/

Failing that just use whatever your favourite graphing program is.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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