On Thu, Apr 28, 2011 at 6:04 AM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Hi Jason,
>
> as you suggested, I am using strip_mask=:200-204:206-8052 to strip my traj.
> I also tried strip_mask='!:1-199,205' or strip_mask='!:1-199,!:205'. Both
> versions work with the ambmask command.
> I can imagine that MMPBSA.py processes the mask with its own mechanism and
> doesn't implement all ambmask features, then this would be understandable.
> Is that right?
>
Elaborating on Bill's response -- MMPBSA.py simply parses the amber masks
from the input file. That is the sole "processing" that MMPBSA.py does for
amber masks. Those masks are dumped directly into ptraj. Note there *may*
be differences between how ptraj parses masks and how ambmask parses masks
(via the atommask module in $AMBERHOME/src/sander), but anything that works
in ptraj will work in MMPBSA.py.
HTH,
Jason
>
> --
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 28 2011 - 09:00:03 PDT
