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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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AutoDock-GPU Virtual Screening #243

Closed apaydinemre closed 9 months ago

apaydinemre commented 1 year ago

Is it possible to do virtual screening using AutoDock-GPU? If possible, how is it done, is there a manual for this? I would be very grateful if you can help me with this. Thank you!

diogomart commented 1 year ago

Hi, yes it is, look up the --filelist option in the README, it enables docking of a batch of molecules. Compiling with OVERLAP=ON has performance benefits.

Other useful options are --contact_analysis 1 and --devnum all.

apaydinemre commented 11 months ago

Thank you very much for your help. Finally I would like to ask you this, I managed to install Autodock GPU, I want to start virtual screening but I think I need to create map files. Do I need to create a separate map file for my protein with each ligand? Is there a way to do this automatically? I don't know anything about map files as I have only done docking with Vina before. I would be very grateful if you could help me.

diogomart commented 9 months ago

See here: https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#optional-generating-affinity-maps-for-autodock-ff

Autogrid can be downloaded at https://autodock.scripps.edu/download-autodock4/

apaydinemre commented 9 months ago

Thank you so much!