AMBER: Water as part of protein in mm_pbsa calculation

From: Yong-Liang Zhu <>
Date: Sat, 11 Oct 2003 20:20:12 -0700

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

Thank you in advance.


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Received on Sun Oct 12 2003 - 04:53:02 PDT
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