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PostPosted: Mon Aug 17, 2009 8:21 am 
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Joined: Tue Jul 21, 2009 10:05 am
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Hello Sir,

I am doing flexible docking in AUTODOCK4.0 [command line]. It took 53+ minutes.

Docking information is follows:-
Receptor – hsg1.pdb
Ligand- ind.pdb
Give flexibility - ARG8 residue

Performance Info:-
Steps----------------------Time-Taken
Ligand Preparation--------2.527s
Receptor Preparation-----3.839s
Flexible Receptor Prep----0.934s
Gpf Step--------------------0.350s
Dpf step--------------------0.736s
AUTOGRID -----------------14.635s
AUTODOCK----------------53m 12.418s
Total-----------------------53m 35.439s


But, in the AUTODOCK site I had read like “high-quality flexible docking can be done in around a minute.”

My AUTODOCK Running system configuration is ->
Intel Xeon Processor, 4 GB RAM, 130 GB HDD

Why my docking take this much time? Any problem with my system configuration or have to add any factures in it?

With Thanks and Regards,
Remya Francis M.


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PostPosted: Mon Aug 17, 2009 10:25 am 
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Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
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But, in the AUTODOCK site I had read like “high-quality flexible docking can be done in around a minute.”


Sorry about the misunderstanding, but something like that would have been on Vina's web site. You are using AutoDock 4, which does tend to be much slower. By the way, "flexible" in "flexible docking" refers to the ligand.

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