David Case or other GB-OBC developer,
I am very interested in using Amber's Generalized Born - OBC implicit
solvent, but I had a couple questions about cutoffs which I hope you, or one
of your associates, could answer for me.
I am mainly wondering how you determine appropriate cutoffs (Amber Users
Guide says cut=16Ang, rgbmax=10-15Ang or default 25Ang). Were these
recommendations based on experiments you did, perhaps calculating error? or
was the implicit solvent parameterized for cutoffs of 16 and 25 Angstroms?
Any information you have on this will be very helpful in choosing cutoffs; I
am trying to simulate a very large molecule, so knowing the shortest and
safest cutoffs will be helpful, but knowing why is even more helpful for
making sure my science is somewhat concrete.
Thank you so much,
David E. Tanner
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Received on Thu Sep 30 2010 - 10:00:05 PDT
