Subject: Another DOCK question

From: Irene Nobeli <[email-masked]>
Date: Tue, 30 Nov 1999 12:20:51 +0000 ("GMT)

Dear CCL readers

Can anyone help with the following? I did a rigid docking calculation
using DOCK4.0 with the following parameters for the ranking of the
resulting orientations:
 total_orientations             500
 rank_orientations 		yes 
 rank_orientation_total 	100
This resulted -correctly- in 100 orientations being ranked in the output
file.

Then I tried to dock the same ligand to the same receptor using a
conformation search for the ligand. I used an anchor search and the same
parameters for the ranking of orientations. However, this time I only get
10 ranked orientations in the output and I don't seem to be able to
increase that. Is there some parameter I should change, or is this a limit
for docking combined with conformational search?

Many thanks, I will report back the answers, if any.

Irilenia

------------------------------------------------ 
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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