AMBER: Added water and mm_pbsa

From: Yong-Liang Zhu <>
Date: Wed, 1 Oct 2003 10:29:37 -0700

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

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 01 2003 - 18:53:00 PDT
Custom Search