[Dock-fans] dock6 speed
sudmukh at yahoo.com
Tue Oct 24 08:15:20 PDT 2006
I noticed you set max_orientations to be only 100, and all the other parameters seem quite reasonable. I do not think dock is running so slow because of the input file. However, dock may take a long time if your SPH file has a large number of spheres. Make sure the docking spheres are actually in the binding site, and the final_spheres.sph has a reasonable number of spheres (consider using sphere_selector with a 10A cutoff).
Apart from that, it is possible that Unix machine you are using might be old and slow. Since it takes 15 mins to read in the grid files, I think reading from the disk might be slow. Could you send the details of the computer you are using to run dock?
----- Original Message ----
From: Rima Chaudhuri <rima.chaudhuri at gmail.com>
To: dock-fans at docking.org
Sent: Saturday, October 21, 2006 10:03:31 PM
Subject: [Dock-fans] dock6 speed
I am trying to test a small sample of 300 molecules using dock6. The speed is unbelievably slow, it takes almost 15 mins to read the frid files and another 45 mins to dock 1 compound. I aim to dock huge databases later. I think I might be doing something wrong
w.r.t the input file, but that i downloaded from the tutorial and made neccessary changes. Am pasting my dock.in for your perusal. Please suggest, as in what might be going wrong?
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