Thanks Jason!
You are right, it is mentioned in -h. I tend to use it all the time, but
this time overlooked it because I was referring to the manual and it wasn't
in there. So I assumed, it won't be in -h either.
Thanks for your help.
Best
Rohit
On 5 November 2013 14:49, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
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Received on Tue Nov 05 2013 - 07:00:03 PST
