Subject: Re: CCL:Solvate organic molecules?

From: David van der Spoel <[email-masked]>
Date: Fri, 26 Jan 2001 10:02:03 +0100 (CET)

On Thu, 25 Jan 2001, Renxiao Wang wrote:

>For some reasons we need to solvate organic molecules or even proteins
>with explicit water molecules. Will anybody recommend a reliable algorithm
>for doing this? It will be ideal if it is able to reproduce the 'real'
>situations. The first layer of water is enough. 
>
>Please note that we prefer an algorithm rather than a certain program. It
>is simply because we are writing programs in our approach. We certainly
>know about some programs, such as AMBER and CHARMm, which can place waters
>around a given molecule. But we are a little bit skeptical for what they 
>generate on the screen.
If this makes you skeptical, then try quantum mechanics or X-ray
crystallography instead. Writing a program in "your own approach" will
certainly not improve the result unless you use a better description
than molecular mechanics (i.e. quantum chemistry).

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++