From chemistry-request@server.ccl.net  Fri Dec 31 13:11:11 1999
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Date: Fri, 31 Dec 1999 12:02:29 -0500 (EST)
From: Joe M Leonard <jle@world.std.com>
Message-Id: <199912311702.MAA16615@world.std.com>
To: chemistry@ccl.net
Subject: Dock VdW parameter question

Folks,

Looking at the Dock 4 VdW parameters, I am not sure I understand
how (for example) the nitrogen parameters are assigned.  There are
three all-atom nitrogen types:

Nitrogen (4 valence)
Nitrogen_quat (4 valence)
Nitrogen_sp3 (3 valence)

Does this mean that all nitrogens are given the first parameters,
unless they're NR4's (which get the second) or NR3's (which get
the third)?  Am I missing something about how things like aromatic
nitrogens are handled?

Joe Leonard
jle@world.std.com

P.S. Best wishes for the holiday season and the new year!


From chemistry-request@server.ccl.net  Sat Jan  1 06:56:05 2000
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Message-ID: <000b01bf5445$fa3c5dc0$3b8506c1@chem.klte.hu>
From: "Tamas E. Gunda" <tamasgunda@tigris.klte.hu>
To: <CHEMISTRY@ccl.net>
Subject: MM3 file format
Date: Sat, 1 Jan 2000 11:50:10 +0100
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Hi Everybody,

Could somebody give me a link where a precise description of MM3 file format
can be found?


Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
L. Kossuth University, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 316666/2472
fax: (+36-52) 512914
e-mail: tamasgunda@tigris.klte.hu
home-page: www.klte.hu/~gundat/gunda.htm