AMBER Archive (2008)

Subject: RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Thu May 22 2008 - 15:37:04 CDT

Hi Marcin,

Not sure this is answered or not ...

The confusion originates from the different default settings in MMPBSA perl
script and sander for nonpolar solvation free energies.

If you turn on the option of NPOPT = 2, you can get desired output without
setting any more parameters, i.e. the default values inside sander
(CAVITY_SURFTEN = 0.04356 and CAVITY_OFFSET = -1.008) are for NPOPT = 2.

All the best,
Ray

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