Hi,

I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules.

When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site.

I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine ‘crystal (or say, ordered) water molecules’.

This presets-interactive 3-hydrophobicity surface seems to perform this function in some way.

Thank you for your help.

Ying-chieh

Ying-Chieh Sun, Professor of Computational Chemistry

Chemistry Department

National Taiwan Normal University

Taipei, Taiwan 11617

Tel: +886-2-7734-6215

Fax: +886-2-2932-4249