AMBER Archive (2002)

Subject: dual H-bonding of bridging waters - CARNAL

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Tue Dec 10 2002 - 18:16:24 CST

Hello,

I was just wondering how I might go about finding 'bridging' waters in
CARNAL analysis of a protein-ligand complex. I have one group that
consists of the protein & ligand atoms. I can then search for h-bonds
between this group and the water, but I only get back a large ammount of
data that corresponds to waters h-bonded to either protein or ligand,
but not both. I would imagine the answer would involve finding all OW
atoms within ~3 angstroms from both atoms of interest. I would really
like to get the occupancies as well.

Any help his appreciated.

Mike Ford