[AMBER] parameters in mm/pbsa calculations

From: Qinghua Liao <fantasticqhl.gmail.com>
Date: Wed, 23 Nov 2011 13:45:42 +0100

Dear amber users,

I have some problems on the parameters in mm/pbsa calculations.


1. The default values of istrng and saltcon are 0.0, but in the python's
tutorial, both of them are set as 0.10, and also sometimes 0.15. So how
should I choose them according to my own system?

2. CUTCAP is set to -1.0, does that mean that the radius of the water
sphere is big enough to enclose the whole solute?

3. What's the default method for nonpolar solvation energy in python's
version? How should I do If I want to set MS==1, just place MS=1 in the
general list?

Thanks very much for any response. 

-- 
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
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Received on Wed Nov 23 2011 - 05:00:02 PST
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