Subject: AUTODOCK 3.0.5

From: Thomas Haselhorst <[email-masked]>
Date: Thu, 17 Aug 2000 11:02:56 +1000

dear all,

i have some problems  running AUTODOCK 3.0.5. i worked with the example
files,
without any problems! but setting up my own protein-ligand complex i
found my ligand not
within the binding site ...rather somewhere in the protein. I increased
the grid space (0.5A) but unfortenuately
without success. in any case the ligand is moving out of the grid.
here are my questions:

1. what can i do to overcome bumbs of the ligand with the receptor ??

2. furthermore, i am interested in docking a carbohydrate into the
binding site
    of an enzyme. it is known from x-ray structure that the ring
conformation of the bound
    sugar is not any longer a  chair conformation. in which way i can
setup AUTOTORS to
    modify the ring conformation ???

thank you very much in advance. I appreciate any help !!!
sincerely yours
Thomas Haselhorst

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Dr  Thomas Haselhorst
Centre for Biomolecular Science and Drug Discovery
Griffith University (Gold Coast Campus)
PMB 50 Gold Coast Mail Centre
Queensland 9726
Australia

email: [email-masked]
http://www.gu.edu.au/centre/cbsdd
Ph:  +61 7 5594 8060
Fax: +61 7 5594 8098
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