igb=8 is not available if you only have AmberTools 1.5. This option is
available if you have Amber 11 because igb=8 is coded into sander, but not
nab (yet).
Also, the internal dielectric was set to have a default value of one because
this best reproduced PB results in water. In general, it is probably best to
use the default value unless you are trying to perform MM-GBSA calculations
using a solvent other than water.
I hope that helps.
-Bill
On Wed, Apr 27, 2011 at 10:48 AM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Hi Jason,
> I have read about the igb=8 option.
> My version of MMPBSA.py tells me that igb=8 is not available.
> Will it run with AmberTools 1.5?
>
> Another question:
> What do you think about the usage of internal dielectrics 2 and 4 in
> MMPB/GBSA calcuations?
> I get results closest to experimental value when using 1.* *But I would
> also
> like to know if there is a profound reason to use 1, I mean, is something
> in
> the procedure parameterized to 1?
>
>
> Greets,
> Oliver
>
> --
> 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Apr 27 2011 - 09:30:03 PDT
