AMBER: Question about determination of hydration points in binding sites

From: Cenk Andac <>
Date: Sun, 27 May 2007 01:51:27 -0700 (PDT)

Dear Amber community,

I would like to determine hydration points in a binding site. Could someone please guide me on how one can determine hydration points from MD trajectory and visualize them in similar spirit to Figure 4 in a research paper entitled

" N. Spackova, T. E. Cheatham, III, F. Ryjacek, F. Lankas, L.v. Meervelt, P. Hobza & J. Sponer (2003). Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4&#8217;,6-diamidino-2-phenylindole and DNA duplexes in solution. J. Am. Chem. Soc., 125, 1759-1769. "

my best regards,



   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey
 Cell: +90-(536)-4813012

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Received on Wed May 30 2007 - 06:07:03 PDT
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