AMBER: residence time& hydration density

From: Andres Palencia <>
Date: Wed, 25 Oct 2006 16:16:53 +0200

Hi Ambers,

I am working with a complex between protein and ligand which has five
water molecules buried at the binding interface. I have mainteined these
crystallographic water and solvate the system with TIP3P water prior to
run MD simulations. Somebody knows how could I calculate the residence
time and the instantaneous coordination number of these water molecules?
It is possible to do it with Amber8?.
Also, I am interested in calculate the hydration density of these buried
water molecules and of specific residues at the binding site, anybody
knows if it is possible to do it in Amber8?

I have found many papers with the theory about these terms, however the
computational methodology is not explained.

Thanks in advance,

Andres Palencia
Structural Bioinfornatics
Biotec-Tu Dresden
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 29 2006 - 06:07:07 PST
Custom Search