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.scripps.edu
phone: (858) 784-9781
fax: (858) 784-8896
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Received on Mon Nov 24 2003 - 18:53:00 PST
