Subject: problem about water in active site

From: maoxiang <[email-masked]>
Date: Thu, 24 Jun 1999 14:03:11 +0900

Hi:
    I am doing some molecular modelling in my Ph.D. work. I have docked
the substrate in the active site, but in the reference, it reports that
there are water molecules involved in the reaction. But the problem is 
the active site and the substract is highly hydrophobic, it have some 
aromatic rings. When I do molecular dynamics with insightII, I put 3-4
layers of water around the complex, fix the parts far away from the
active site. but the water all escaped at the end.I know I can tether
the water molecules, but I do not know the exact position.Does anyone
has the experiences to find the proper water positions. I will summarize
the answers. Many thanks. 

With best regards,

Mao

  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|  Mao Xiang                                                      |
|  Lab of Molecular Regulation for Microbial Secondary Metabolism |
|  Shanghai institute of Plant Physiology, Academia Sinica        |
|  300 Fenglin Road, Shanghai, China, 200032                      |
|  Tel: +86-21-64042090-4791                                      |
|  Fax: +86-21-64042385                                           |
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