AMBER Archive (1999)

Subject: how to find water in solute in a long trajectory?

From: Jianxin Guo (jguo_at_zeeman.unmc.edu)
Date: Tue Nov 16 1999 - 23:18:00 CST

Hello,
    are there any easy way to find waters in cavities of solute? One
way that I can think out is to find the hydrogen bond occupied
percentage of one water with two or more sulute atoms in the trajectory,
and then to monitor the hydrogen bond distance with time. Are there any
other easy way to do that?
Thanks.
Jianxin Guo