Dear Jason
> I'm actually not sure what the PB folks use for their calculations. Does
> it say somewhere in the manual?
As for igb = 2 option, you can find a comment to use "set default PBradii
mbondi2" in p.56 of the Amber11 manual (Probably you may know.)
This is a reason I 've got confused as working with the tutorial.
In the case of PB calculation (ipb = 1) combined with radiopt = 0, there is
no comment requiring to modify radii in the Amber
Tool manual. As far as I understood, topology files can be built without
modifying radii according to the directions of tutorial 3.
Toshi Yui
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Received on Wed Dec 21 2011 - 01:30:03 PST
