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’,6-diamidino-2-phenylindole and DNA duplexes in solution. J. Am. Chem. Soc., 125, 1759-1769. "
my best regards,
jenk
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
E-Mail:cenk_andac.yahoo.com
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Received on Wed May 30 2007 - 06:07:03 PDT
