AMBER Archive (2003)

Subject: AMBER: Re: AMBER water mediated contacts

From: Rhonda Torres (torres_at_scripps.edu)
Date: Mon Nov 24 2003 - 11:51:31 CST

Hi Vlad,

Visual inspection of the system will give you a general idea if a
water mediated contact occurs between the RNA and protein. From
there you can use ptraj with closestwaters to select the closest waters
to the amino acid or nucleotide of interest.

Hope this helps.

Rhonda

Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

email: torres_at_scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896
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