AMBER Archive (2006)

Subject: AMBER: residence time& hydration density

From: Andres Palencia (andresp_at_biotec.tu-dresden.de)
Date: Wed Oct 25 2006 - 09:16:53 CDT

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
andresp_at_biotec.tu-dresden.de
Structural Bioinfornatics
Biotec-Tu Dresden
Germany
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