ADL: Simulation Time

Diogo Santos Martins diogom at scripps.edu
Sun Nov 22 10:38:24 PST 2020


Hi Joey,

The runtime of Vina depends mostly on the number of ligand atoms and number of ligand rotatable bonds. What you describe could happen if one has a very large ligand or docks the protein onto the ligand by mistake.

Best regards,
________________________________
From: autodock-bounces at scripps.edu <autodock-bounces at scripps.edu> on behalf of Joey Farrell <jpfarrell at uchicago.edu>
Sent: Saturday, November 21, 2020 11:39 AM
To: autodock at scripps.edu <autodock at scripps.edu>
Subject: ADL: Simulation Time

Hello everyone,

I have run into a peculiar issue simulating a ligand docking interaction at one specific site of my macromolecule. I docked my ligand at 9 different sites and allowed the simulation to carry out for 36 hours each. However, the first site was no where near able to finish in this amount of time; it was projected to take about 180 hours instead. Because this is not feasible, I went as far as reducing exhaustivity from ~16 or 24 down to 1 and reduced the docking grid from 40 x 40 x 48 to 5 x 5 x 5. However, this has had no noticeable impact on the rate—it still looks as though it would require the same 180 hours to run to completion.

Is this indicative of some sort of error in the setup? What could be the potential cause of the simulation at this particular centre being so computationally taxing, even when the chosen pocket radius and exhaustivity have been reduced drastically?

Thank you so much,
Joey
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