AMBER Archive (2003)

Subject: AMBER: Water as part of protein in mm_pbsa calculation

From: Yong-Liang Zhu (yzhu_at_plexxikon.com)
Date: Sat Oct 11 2003 - 22:20:12 CDT

Dear Amber users;

I'm relatively new in understanding mm_pbsa calculation. I identified 3
water molecules from trajectory that mediate ligand-protein binding (i.e.,
have H bond with both ligand and protein). So I included those three waters
as part of protein for mm_pbsa calculation. However, the change in binding
energy became worse (more positive delta G). So anyone has clue why this
happened?

Thank you in advance.

Yong

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