[Dock-fans] Regarding Screening of 7000 ligand molecules in DOCK6.7 in serial gnu.

Trent E. Balius tbalius at aol.com
Tue Jun 30 10:30:45 PDT 2015

 Hi Satheesh,

Do any files get written out? What is in your output files?  It might help if you send your input file. 

I might suggest for you not to rank order the molecules by score during the docking run.  
This way molecules are written as soon as they are docked.  

[You may want to run dock a second time to rank order your molecules (just rescore and rank do not sample). ]

If we assume that each molecule will take 1.4 min per-molecule then then this calculation will take about 7 days to run: 

 7000 molecules * 1.4 (min/molecules) * (1 hour/ 60 min) * (1 day/24 hour) = ~7 days

I would sujest that you do not dock very flexible molecules (e.g > 8 Rotatable Bonds).
You may want to use the database filter to remove these molecules on the fly. 

I hope that this helps,


Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: Garisekurthi Satheesh <gschembio at uohyd.ac.in>
To: dock-fans <dock-fans at docking.org>
Sent: Tue, Jun 30, 2015 9:41 am
Subject: [Dock-fans] Regarding Screening of 7000 ligand molecules in DOCK6.7 in serial gnu.

Hello Everyone,      
I have query, regarding the 7000 ligand molecules docking in the serial gnu. I do not have cluster (parallel gnu), so how could I do above number (7000 molecules) in serial gnu of DOCK6.7. When I submit serial dock6, after some time it get stopped without any error. Could you please suggest me, how can I tackle this without parallel gnu (I mean serial gnu of DOCK6) ?     
Please kindly give me your answer.    
Thank you,   

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