AMBER Archive (2008)

Subject: AMBER: GB offset for proteins

From: Sally Pias (sallypias_at_gmail.com)
Date: Sun Dec 07 2008 - 23:14:58 CST

Hello,

Tutorial A4 points out that offset=0.13 with generalized Born (GB)
implicit solvation gives results closest to Poisson-Boltzmann for
nucleic acids (Tsui and Case, JACS 122, 2489, 2000). Has such an
optimum offset value been determined for proteins? Is the default,
offset=0.09, appropriate to use for NMR refinement (simulated
annealing) of a protein?

Thank you,
Sally Pias
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