Yes, MMPBSA.py has its own way of parsing the strip_mask variable that is
separate from the ambmask command. Thus, not all ambmask features are
supported by MMPBSA.py.
-Bill
On Thu, Apr 28, 2011 at 9:04 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?
>
> --
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 28 2011 - 06:30:06 PDT
