I had the same issue which made me exhausted while doing flexibke docking. Thank God, got the free trial version of schrodinger package which solved many problems. I will suggest you to plz change your approach
I am using PyRx tools for the past 6 years. regularly you have to clear the old files that are uploaded in the PyRx tool and in your PC, please clear the data from this folder C:\user\.mgltools\PyRx - \Macromolecules & Ligands & etc
if an application is crashing again uninstall the program and re-install it.
I'll just highlight that I didn't experience these issues with my PC.