AutoDock GPU Batch Docking Result Unreproducible #262
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Hello, |
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Do you need my Ena116776.pdbqt and the receptor's maps file? |
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Yes, that can be useful. Thanks! |
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I found out that it could be due to the reason that I commented out some lines in the maps file. I will investigate it myself first and update here if I figured out what went wrong. |
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Ok. Thanks. Let us know. |
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Dear Developers,
As always, thanks for the amazing program. I am running the latest AutoDock GPU on a Ubuntu system with 3 Nvidia A40. I complied the AutoDock GPU with
overlap = 'on'andNUMWI=256.Because I am trying to do a multi-stage docking, I first docked 120000 ligands with the following command:
autodock_gpu_256wi -B firstBatch.txt -x 0 --nev 3000000 -E 20000000 -n 50 -D all. And I selected the top 1% of the ligands from the first batch based on the docking scores and ran the following command:autodock_gpu_256wi -B secondBatch.txt -x 0 --nev 3000000 -E 20000000 -n 100 -D all, where I changed the # of runs.The top ligands in the first batch were the following:
For the second batch, the top ligands were the following:
It seemed very strange to me that, after increasing the # of runs from 50 to 100, the lowest energy among second batch docking simulations was only -11.46, which showed a great difference from the first batch. I understand that of course variation occurs due to randomness in searching and increase of runs, but how come a subset from the first batch has no ligand with energy lower than -12 after the # of runs was increased to 100, whereas the first batch had many? So I compared the performance of Ena116776 in the first batch and the second batch:
first batch run result for Ena116776:
second run result for Ena116776:
Again, I understand that variation exists due to randomness in searching. However, it can be clearly seen that among the 100 runs, the program failed to find any docked pose that is better than the worst docked pose (-9.35) in the first batch run result. I tried to run docking on this ligand (Ena116776) only, and I tried so many time, none of them could have a value comparable to -14 (I even tried to replicate by using the random seed in the first batch dlg file ). This does not make much sense to me because my search space is not large.
I am wondering whether batch docking mode with 3 cards has a different calculation scheme compared to docking ligands one by one. Please let me know if my problem description is not clear or detailed enough.
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