[Dock-fans] Could not find a valid orientation

[Sudipto Mukherjee]

Dear Xinyu,

As you are in the Stony Brook AMS 536 class, please ask me directly in
class, or email me if you have problems while running DOCK. 
I would be happy to examine your setup in class next Monday and figure out why DOCK is running out of memory for your protein.

 Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University



________________________________
From: Xinyu Guan <bioguan at gmail.com>
To: dock-fans at docking.org
Sent: Friday, March 13, 2009 2:39:30 AM
Subject: [Dock-fans] Could not find a valid orientation


Hi, all,  
I have met several problems when I conducted docking.
 
First, when I ran dock6, the program stopped spontaneously and the .out file said:
--------------------------------------------------------------------------------------------
ERROR:  Could not find a valid orientation.
         (For rigid docking the sought orientation is the whole ligand;
         for flexible docking the sought orientation is the anchor.)
         Confirm that all spheres are inside the grid box
and that the grid box is big enough to contain an orientation.
-----------------------------------------------------------------------------
The second problem is, when I tried to screened out some ligands form a large mol2 (contains 1000 zinc ligands), the program would stop with 
------------------------------------------------------------------------------------------------
Error: memory exhausted!Segmentation fault.
------------------------------------------------------------------------------------------------
 
Thank you very much!


      
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