AMBER Archive (2008)

Subject: AMBER: PCAL and polar contribution in the output file

From: Neha Gandhi (
Date: Fri Jun 13 2008 - 00:42:54 CDT

Hi All,

In MM-pbsa analysis, the ouput consists of corrected reaction field
energy. I am able to calculate non-polar contribution which is
PBSUR=surface area*0.00542+0.92. Where is the electrostatic solvation
energy in the output file such as snapshot_rec.all.out? I cannot
correlate PBCAL with corrected reaction field energy. I appreciate if
somebody can help me to calculate PBSOL for each snapshot. How PBCAL
and corrected reaction field energy are related?

Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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