AMBER Archive (2008)

Subject: AMBER: RE: Request

From: Ross Walker (
Date: Fri Mar 07 2008 - 14:38:25 CST

Hi Delwar,

I am copying this message to the amber mailing list where such questions
should be posted for others to see - please subscribe - see for details.

> I am trying to analyze the data from amber output file. I
> make a new directory
> and put the out put file in the new directory. I also put the
> process_mdout.perl in the same directory. Then I used
> Titan[12] delwar$ process_mdout.perl pnbCE.md10.out &
> I got the following message.
> -bash: ./process_mdout.perl: Permission denied
> I therefore request you to help me where and how I need to down the
> process_mdout.perl and then use it for analyze data.

Under Unix / Linux a file has to be executable for you to be able to run it
with ./foo

Do the following:

chmod u+x process_mdout.perl

and then try again. Alternatively you can do:

perl ./process_mdout.perl pnbCE.md10.out

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to