[AMBER] active site water cluster analysis

From: Ahmet yıldırım <ahmedo047.gmail.com>
Date: Tue, 3 Jun 2014 12:41:47 +0300

Dear users,

I want to do the active site water cluster analysis of a structure. From
paper (http://www.ncbi.nlm.nih.gov/pubmed/19634894):
The active-site water cluster is defined as a continuously hydrogen-bonded
network of water in which (a) the donating and accepting oxygens are within
3.5 Å of each other; (b) the acceptor oxygen and the donating oxygen's
hydrogen are within 2.5 Å; and (c) an angle of less than 120° exists
between the donating oxygen-donating hydrogen vector and the donating
oxygen-accepting oxygen vector.

I have the following questions:
1) How will I pick the active site (aminoacids+waters) from all structure?
2) To do the Active Site Water Cluster Formation and Lifetime Analysis, how
can I apply above (a), (b), and (c) items at the same time using Amber?

I would appreciate any suggestions.

Thanks in advance.

Ahmet Yıldırım
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Received on Tue Jun 03 2014 - 03:00:02 PDT
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