AMBER Archive (2007)

Subject: AMBER: Question about determination of hydration points in binding sites

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sun May 27 2007 - 03:51:27 CDT

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_at_yahoo.com

       
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