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This is my first time using askUbuntu, so I hope I’m doing this right (and please tell me if I’m not!).

I recently purchased a mini computer to run some receptor-ligand docking experiments from home. I have successfully installed the relevant programs (autodock4, autogrid4, and mgltools) on my system. When I open autodock tools from the terminal (a GUI for running autodock that displays interactive graphics of your protein), the window pops open, no problems. However, when I attempt to do anything that causes the graphic of the protein to change (e.g. read in a protein, remove waters, add hydrogens, fix broken residues, or even simply select residues and/or ligands and rotating the protein), the program lags like crazy. Sometimes it crashes, but most of the time it just takes a long time to do anything. For example, it can take upwards of 5 minutes to read in a protein from a .pdb file.

When I look at CPU usage (htop), it doesn’t seem particularly stressed (maybe 10%). When I look at the GPU (radeontop), it’s basically pegged at 100% usage. The underlying autodock program seems fine, as I’m able to run via the command line without issue. I’ve run autodock tools on other machines that seem no more powerful than what I’ve got and the program runs just fine. Furthermore, pymol works as expected on my mini computer with no major issues or slowdowns and with reasonable GPU and CPU usage (not that I know if that’s a fair comparison). I'm inclined to blame my integrated GPU, but supposedly it's capable of running modern triple A games (not that I've tried), so I would think displaying a protein would be well within its capabilities. For what it's worth, I've reached out to the autodock folks as well as AMD to improve my odds of learning something useful.

Do you have any thoughts as to what might be the problem? Is my GPU just not good enough? If so, can I bring down the graphical quality to make things easier on the GPU? Is it possible that autodock tools isn't using my GPU properly in some way? How could I check? Might I have a driver problem? I'm a bit of a novice with all this, so apologies if I've left anything out or if anything is unclear. If there are any additional details that would be useful to provide, please let me know!

Tech Specs: MoreFine S500+ AMD Ryzen 9 5900HX (8 core, 16 thread) w/ Integrated Radeon Graphics (8 core, 2100 MHz) 1 TB SSD 64 GB RAM 64-bit Ubuntu 22.04.2 LTS X11 Windowing MGLTools 1.5.7, patched (I’ve tried 1.5.6, patched and the unpatched versions of each too, same problem occurs)

Thanks Folks! -Triazine

Triazine
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I figured it out! I'm answering here in case anyone else has the same problem. I'll do my best to make clear what I did to fix it, but I probably can't explain why it works very well. I'm also citing and linking to various other AskUbuntu answers along the way, so hopefully that's okay. Here goes...

There is apparently an unmet dependency in Ubuntu 22.04 and AMD's GPU Driver that causes issues with python. There seems to be some debate about whether AMD has fixed it or not, but it definitely wasn't fixed for me. If you'd like to read more about it from folks who know more than I do, go here: Unmet dependencies ubuntu 22.04 & amdgpu HIP support

I proceeded to download the non-HWE AMD Driver (https://www.amd.com/en/support/linux-drivers).

I then followed the install instructions (https://amdgpu-install.readthedocs.io/en/latest/) until I used the amdgpu-install command. At this time, I received an error having to do with something called xorg-video-abi-24.

I then executed cloudqq and Bengt's suggestion from the previously linked AskUbuntu page in which the word "focal" is changed to "jammy" in two files. Before doing this, it is necessary to make the two files editable by the user (see Drew Anderson's answer here: How can I modify a file that is owned by root?)

And now AutoDockTools works great! I hope this helps other folks who run into this issue!

Thanks, -Triazine

Triazine
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