For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have missed some important stuff?
As I’m on the later 64-bit OS, I’m unable to run MGLTools. As a workaround, I’ve been using a Remote Desktop to Windows 10 computers at my university campus in order to prepare .PDBQT files in AutoDock Suite 4.2.6 as well as setting my grid parameters. I can’t manage to get any output from AutoDock Suite as it keeps throwing out errors when I try to run AutoDock with my generated .DPF and .GPF parameter files. Also, as you can imagine, running this software through an emulator/remote desktop is a pain in the ****.
I’m wondering if there’s any possibility that I could convert my .PDB input files into .PDBQT without the need to use Windows/older macOS versions. I’ve tried Virtual Machines but they’re equally painful and I want to streamline the process because my mouse function gets pretty messed up through emulators and such.
My methodology up to this point has been:
– Using Windows 10 remote desktop, download PubChem ligand and RSCB protein files, then reformat the ligand in PyMOL to .PDB
– Format the ligand and protein in AutoDock Suite as .PDBQT (removing waters/solvent, adding polar hydrogens etc first)
– Have a play with Grid Box parameters in the binding site, then writing a conf.txt file for the Vina input
– Transfer .PDBQT files and conf.txt to my native macOS drive
– Run Vina in Terminal
– View output file in ChimeraX
I want to have a more streamlined process to eliminate potential for error that comes with hopping between different software and operating systems. I’ve tried ADFRSuite, but I keep getting segmentation fault errors🥲.
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