Subject: Dock and lone pairs

From: Irene Nobeli <[email-masked]>
Date: Wed, 24 Nov 1999 11:49:47 +0000 ("GMT)

Could any Dock 4.0 user please help me with this?
I am one of these unfortunate people who try to use DOCK 4.0 without
having Sybyl available to prepare the receptor and ligand files. I tried
to use InsightII instead but I ran into the following problem: I load the
protein (receptor) in InsightII, add hydrogens, and attempt to assign
charges using the AMBER force field. However, charges seem to be only
properly assigned, if I also allow lone pairs to be added. Can DOCK deal
with lone pair sites? Am I supposed to use this mol2 file (with H and lone
pairs) in the grid calculation, and then use the original (with no H and
no lone pairs) for docking? 
Also, if anyone knows a discussion list for DOCK users, could they please
send me an address?

Thanks for your time

I. 

------------------------------------------------
Irene (Irilenia) Nobeli
Biomolecular Structure and Modelling Unit
Department of Biochemistry and Molecular Biology
University College London
Darwin Building
Gower Street
London
WC1E 6BT

[email-masked]
0171-419 3890
0171 504 2171

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