AMBER Archive (2003)

Subject: AMBER: Added water and mm_pbsa

From: Yong-Liang Zhu (yzhu_at_plexxikon.com)
Date: Wed Oct 01 2003 - 12:29:37 CDT

Hello all,

My system includes a protein and a ligand. I tried to use mm_pbsa to
calculate binding energy of the ligand to the protein. I manually added 8
water molecules in the pdb file before I used tleap to add water cap. Then
mmpbsa calculation seems to include those manually added 8 waters in the
calculation.

The reason I added waters in addition to tleap water cap is that those
waters mediates interaction between ligand and protein and tleap cannot add
water to those 8 positions.

Do anyone has similar experience? A more general question is how to include
water molecules as part of protein to calculate binding energy using mmpbsa?

Thank you in advance for your assistance.

Yong

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