[Dock-fans] anchor orientation

Trent E. Balius tbalius at aol.com
Tue Apr 27 06:27:50 PDT 2010


 
 Hi Dariusz,
    
You can turn off ligand orientation by the following:
  
  orient_ligand    no
  flexible_ligand  yes

This will grow out your ligands starting from the anchor in your beginning orientation. 
In the Rizzo group, we call this procedure Fix Anchor Docking. 
  
 
Note that the anchor will still move because of the simplex minimizer. 
    
I hope this helps, 
  
 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
To: dock-fans at mailman.docking.org
Sent: Tue, Apr 27, 2010 5:10 am
Subject: [Dock-fans] anchor orientation


Dear all,

I have a question related to anchor and grow algorithm as implemented in
DOCK 6.3.
Would it be possible to use user defined orientation of the anchor ?
In other words, I would like to start with predefined coordinates of the
anchor and then use DOCK
for growing the layers.
I assume it would require modifications in the source code,
any hints ?

best,
Dariusz Ekonomiuk

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