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
http://ambermd.org).
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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 07 2014 - 05:00:03 PST
