AMBER Archive (2008)

Subject: AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query

From: Ross Walker (
Date: Thu Nov 06 2008 - 02:18:22 CST


Dear Zgong,


I am copying this message to the amber mailing list which is the best place
for such queries - see for details on how to sign up.


With regards to > process_mdout.perl ../polyAT_vac_md1_12Acut.out




perl process_mdout.perl ../polyAT_vac_md1_12Acut.out


if you get


> perl command not found.


Then you will need to install perl on your machine. Try 'yum install perl' -
I think that will work on Ubuntu.


All the best



From: zgong.hust []
Sent: Thursday, November 06, 2008 12:09 AM
To: amber_tutorial_query
Subject: Poly(A)-Poly(T) DNA Tutorial Query


Dear sir:

       I have read your amber tutorial for beginners. I have some problems
when I repeat the example.

After I finished the molecular dynamics about the DNA and analyse the energy

I type the command


mkdir polyAT_vac_md1_12Acut
cd polyAT_vac_md1_12Acut

process_mdout.perl ../polyAT_vac_md1_12Acut.out


However, it doesn't work. I have download your perl script, but I don't konw
how to use it. Could you help me about this?

My system is Linux Ubuntu 8.04

My PC hardware is P4 3.0GHZ

Thank you for your help

your sincerely

Zhou Gong

Huazhong University of Science and Technology





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