ADL: large ligand

Amr AL-HOSSARY amr_alhossary at
Mon Dec 15 18:23:11 PST 2014

I think Vina can be used, but it would consume a tremendous amount of time. 

Also QuickVina 2.1 (under development) can be.
May you send me the protein and the ligand?



Best Regards, 

Amr Ali AL-HOSSARY |   Ph.D. Student | International PhD program in
Computational Biology and Bioinformatics | School of Computer
Engineering |   Nanyang Technological University | Singapore (GMT+8)
|  Email:  aalhossary at |  Mobile: +65-94572816 

-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at] On
Behalf Of f.namazifar at
Sent: Tuesday, December 16, 2014 6:00 AM
To: autodock at
Subject: ADL: large ligand

Hi. I want to do protein-ligand docking. But the ligand is large and
flexible  with 546 rotatable bonds set TORSDOF 546. I have two questions:
1- When I used autodock4.2 I received this error:"too many torsions.  
maximum number of
torsion is 32". How can I solve this problem?
2- Can I use vina for this system?
Best Regards.

University of Isfahan (

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