AMBER Archive (2008)

Subject: AMBER: the question about "RADIOPT" option in mm_pbsa

From: TaoPaul (
Date: Sat Oct 25 2008 - 06:11:04 CDT

Hi, all
In amber9 user mannual RADIOPT=0 means "use radii from the prmtop file for both the PB calculation and for nonpolar solvation energy calculation", while RADIOPT=1 " instructs sander to use van der Waals radii from the promtop file for nonpolar solvation energy calculations" (Page 126). So what the difference between the "radii" and "van der Waals radii" since two options are emphasized to be different in calculating the nonpolar solvation energy. " Is the 'van del Waals radii' the optimized radii by Tan and Luo? I guess it is from the other part of the mannual, "the radii set optimized by Tan and Luo to mimic Gnp"(Page 271) But I am not sure. Could someone give me an explanation?
Best wishes!
Paul Tao
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