From: Jason Swails <>
Date: Fri, 07 Nov 2014 07:31:14 -0500

On Fri, 2014-11-07 at 14:30 +0530, Ruchika Bhat wrote:
> Thank you sir but* still its not working.*
> I am using AMBER 10
> The error that is getting generated is:
> [ruchika.coe SIMULATION]$ $tleap -s -f leaprc.ff99SB

Get rid of the $. That makes the shell look for a shell variable or
environment variable called tleap. Since you never defined that, it is
simply blank, and the shell interprets your command as:

-s -f leaprc.ff99SB

> -bash: -s: command not found

And as you can see, bash does not know what to do with "-s".

> [ruchika.coe SIMULATION]$ $tleap -f leaprc.ff99SB
> -bash: -f: command not found

Nor does it know what to do with "-f"

> [ruchika.coe SIMULATION]$ $tleap leaprc.ff99SB
> -bash: /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc.ff99SB:
> Permission denied

And here it just tried executing leaprc.ff99SB, which does not have
execute permissions.

However, I would strongly encourage you to upgrade to AmberTools 14
(which is open source and free to download from
Amber 10 is now over 6 years old and no longer supported. You will have
much better luck with the tutorials and getting help from the list if
you are using the latest versions of the Amber software.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Nov 07 2014 - 05:00:03 PST
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