Subject: Delphi Calculation of interaction energies

From: Michal Boháč <[email-masked]>
Date: Wed, 5 Mar 2003 18:19:17 +0100

Hi everybody,
Currently I'm solving the problem of calculation of the electrostatic 
interaction energies between two distant charged residues in the protein. 
I had found the theoretical possibility of such calculation including the 
solvent effect using the PB equation in the Delphi package as is shown in 
the its examples of Subtilisin (example from version 3.0). 

I have crucial question concerning this proposed methodology:
 
I would like to calculate the electrostatic interaction between all charged 
residues and halide ion, which is noncovalently bound in the active site 
of the haloalkane dehalogenase protein. Halide is hetero-atom in this case
being an intermediate of the enzymatic reaction. I'm trying to find its
stabilization by charged protein residues...
Is it possible to perform such calculations with heteroatom using current 
Delphi 4.0 package? I would like to include into the active also two 
experimentally known catalytic waters (essential for hydrolysis), affecting 
the electrostatics of the enzyme active site....is it possible to include them too?

Does anyone have any more experiences in calculation of such electrostatic
interactions using using Delphi?  If anyone will be interested in this general 
question I can write him more details concerning this study. 
Any comments and ideas or help will be greatly acknowledged ;-)

Best regards,
Michal
 
**************************************************************
   Michal Boháč, MSc.
**************************************************************
   student at
   National Centre for Biomolecular Research
   Faculty of Science, Masaryk University
   Kotlářská 2, 611 37, Brno
   Czech Republic

   email: [email-masked]
   URL:   http://ncbr.chemi.muni.cz/~bogey
   phone: +420-541129377
   fax:   +420-541129506
   cell:  +420-604747103