AMBER Archive (2008)

Subject: AMBER: energy pairwise decomposition in GB/SA simulation

From: wfli_at_biophy.nju.edu.cn
Date: Wed May 28 2008 - 05:29:42 CDT

Dear ambers,

I need to decompose the total energy of the GB/SA simulation into
pairwise residue interactions. I noticed that AMBER can do this if the
option IDECOMP is switched on. In this case, the option GBSA should be
set to "GBSA=2", namely, the SASA is computed by ICOSA method instead
of LCPO method. I'm trying to understand how this ICOSA method works,
and also how the decomposition is performed. Could you tell me which
papers I should refer to understand these processes?

Thank you very much in advances.

Best wishes,
Wenfei Li
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