Subject: MD simulation of protein-inhibitor

From: Bookworm <[email-masked]>
Date: Wed, 10 Jan 2001 17:57:37 +0800

Dear colleagues:
	I want to study the interactions of a protein-inhibitor 
complex by MD simulation. The protein is a serine protease and the
inhibitor is:
	Methoxysuccinyl-Ala-Ala-Pro-NH-CH-B(OH)2
                                       |
                                       CH3
	I have following two questions:
	1. There are not a atom type \"B\" and the buiding block of 
-NH-CH(CH3)B(OH)2 in the force field. Can anyone suggest a way to 
get the parameters of \"B\" and the building block.
	2. There exists a covalent bond between protein and inhibitor
(between \"o\" of Ser195 in the protein and \"B\" in the inhibitor). How to
arrange this case? 
	Thanks for your kind help in advance and all replies will be 
promptly summarized.

Best wishes
Zhiyong Zhang, Ph.D
School of Life Science in USTC
Hefei, Anhui, PRC    

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