On Tue, 2013-11-05 at 14:18 +0100, rohitarora10.gmail.com 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 MMPBSA.py 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:
MMPBSA.py -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.
HTH,
Jason
P.S. This flag is listed by using "MMPBSA.py --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
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 05 2013 - 06:00:02 PST
