[Dock-fans] Can dock5 recognise the cofactor FAD?

Philip Crawford p.crawford at unsw.edu.au
Wed May 24 18:34:05 PDT 2006


Irene,
I've been looking at what I think is the same molecule and have not had any problems with generating molecular surface, spheres or grids with FAD included.
>From the Dock 4 manual (p. 20):
(Note - sometimes, as in the case of a cofactor or catalytic metal ion, it may make chemical sense to 
keep a ligand in the PDB file.)
 
I think you may have read this advice to remove all HETATM's in the tutorial. That was probably correct advice for the target specified in the tutorial. I couldn't find any reference to HETATM in the Dock 5.3 or 5.4 manuals.
 
Cheers,
 
Phil Crawford
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Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
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Email: p.crawford at unsw.edu.au
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From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org] On Behalf Of irene xue
Sent: Wednesday, 24 May 2006 10:33 PM
To: dock-fans at docking.org
Subject: [Dock-fans] Can dock5 recognise the cofactor FAD?


Dear all,
 
When I read the dock5.3 manual, I find that all HETATM lines in the PDB file should be removed. Now, there is a cofactor FAD in my protein file and FAD will affect the interaction between the ligand and the receptor in the binding pocket.  My questions are
 
1) Can dock5 recognise the cofactor FAD?
2) If not recognise, how to deal with this cofactor?
 
Thanks a lot.
 
                                                      irene
 


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