AMBER: RE: Contact TSRI: Ross Walker

From: Ross Walker <>
Date: Wed, 25 Jul 2007 08:31:53 -0700

Dear Manvendra

Please post these types of queries to the amber mailing list/reflector in
future - see for details of how to sign up.

> I m a new user to AMBER. I am using your tutorial for simulation and
> analyzing DNA polyA-polyT Decamer.
> i have reached to the chapter 3.3 (-analysing the result).
> i want to know that do i have to use pearl script for analysing the
> simulation result?

You don't have to use the perl script - you can analyze the result any way
you want. Even better would be if you wrote your own perl script or similar
analysis script in a language of your choice since then you'd get a much
better understanding of everything.

> if yes , then i want to know will AMBER 8 OR 9 provide this pearl
> script in support to run analysis?
> or i have to download it ?

You need to download it. See section 3.3.1 where there is text which says:

If you are working on this tutorial on your own machine then you can
download the perl script here.

Click on the "here" and you can save the perl script to a directory of your

For reference the path to the script is:

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Jul 29 2007 - 06:07:12 PDT
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