Re: [AMBER] Location of MMPBSA temporary files

From: Jason Swails <>
Date: Tue, 05 Nov 2013 08:49:50 -0500

On Tue, 2013-11-05 at 14:18 +0100, wrote:
> Dear Amber users,
> Is there a flag that can be used to define the location of the temporary
> files that are generated during MMPBSA run? (example:
> _MMPBSA_complex_gb.mdout.0 etc.)
> I am writing a shell script to run on multiple protein systems.
> If I run the script corresponding to protein#1, and then run it for
> protein#2, it gives an error for protein#2

You can manually set the prefix of the temporary files. The default is
_MMPBSA_, but you can change it to whatever you want. This can be used
to specify a new location if you wish by making the prefix something
like mydirectory/_MMPBSA_ or you can just call it _MMPBSA2_,
_MMPBSA3_, ... etc. Specify the prefix with the "-prefix" flag: -prefix _MMPBSA2_ -i ... etc.

> "LengthError: length mismatch in energy vectors"
> I believe this is because #1 is still running and their temporary files are
> stored in the same location, hence there is a conflict.

Yes, this would be a problem.

> Better still, is there a way to NOT generate any temporary files during
> MMPBSA run? If a run fails, I can always deal with it separately.

No. If it was possible to avoid generating temporary files I certainly
would have done so :). In fact, data is exchanged via pipes wherever
possible specifically to avoid creating more temporary files.


P.S. This flag is listed by using " --help". If you're not
already in the habit of trying --help or -h when you have a question
about a program, I highly recommend it. I have learned many things
reading help menus and man pages.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Nov 05 2013 - 06:00:02 PST
Custom Search