[Dock-fans] Distorted bond Angles

Trent E. Balius tbalius at aol.com
Fri Jun 10 07:03:43 PDT 2011

 Hi Marco,
One approach to sample this distorted torsion is to modify the flex.defn and the flex_drive.tbl files.
See the following:
In addition consult the following:

Excerpt from flex.defn:
name sp3-sp3 
drive_id 3 
minimize 1 
definition .3 [ 3 H ] [ 3 O.co2 ] 
definition .3 [ 3 H ] [ 3 O.co2 ] 
Here you can see the the flexible definition file specifies a torsion angle and gives the drive type (drive_id). 
  Excerpt from flex_drive.tbl
drive_id 3 
positions 3 
torsions -60 60 180 

Here you can see that the flexible drive table specifies the angle to be sampled for the drive type.

You should modify the flex.defn to have an entry for the olefine bond and use of create an appropriate entry in the flex_drive.tbl file.
You may want to also verify that your small molecule mol2 file has the correct hybridization and protonation.  

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: Marco <marco at chimfarm.unipg.it>
To: dock-fans at mailman.docking.org
Sent: Fri, Jun 10, 2011 8:43 am
Subject: [Dock-fans] Distorted bond Angles

Hi all!
I'm a new dock user. Following the tutorial I've performed docking studies
on my target. I'm actually docking a small molecule with a cinnamic acid
moiety in a flexible way. Unfortunately the olefine bond in the docking
solution is distorted in an unnatural manner. To overcome this problem I can
dock in the rigid way the conformers of my small molecule, but I'd like to
know if there is a way to set manually as rigid bond some bonds of my

Any advice is very appreciated. 
Thank you.


Marco Cellanetti, 
PhD Student.
Bachelor Degree in Medicinal Chemistry and Technology of Drugs

University of Perugia
Department of Medicinal Chemistry and Drug's Technology
Via del Liceo, 1 - 06123 Perugia (Italy)
Tel ++39 075 585 5169/5114

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