Hi, guys. I started doing some dockings a few days ago and there was an constantly error showing up on the autodocktools cmd:
"swig/python detected a memory leak of type 'BHtree *', no destructor found." (PFA a printscreen of the error).
The error kept showing up after every command i gave. For example, after every missing atom added it showed up again. I didn't mind at first, because everything was working just fine, even though I was wondering if my results would be realiable with such an error.
But now, there is another error showing up on the autodock (You can also find a printscreen attached), and i can't dock anything anymore. I have already tried reinstalling autodock and MGLtools.
Has anyone had this same errors? Would you know how can I solve it? Just making clear that I'm not familiar with programming.
Thank you so much!
Autodock4 makes use of python programming language to run their commands and thus any error you encounter comes from the script. Sometimes during atom fixing, the python script pops up due to the size of your protein (especially when amino acids are greater than 200). This is one of the limitations of using autodock4 for fixing atoms.
In the second case, there's a memory leak in your version of python your computer system uses and this might not be compatible with Autodock4 python's script. To learn more about python memory leak and how to solve this, see the attached link
https://www.section.io/engineering-education/how-to-fix-memory-leaks-in-python/
Hi, Abdeen Tunde Ogunlana . Thank you for you answer! I'm going to read the article you send and try to solve the problem.
About the limitations of using autodock for fixing atoms, would you suggest any other software for this task?
Yes, I have used schrodinger software (maestro; protein preparationwizard module) to overcome this limitation. But it's unfortunate that the free license of maestro cannot do this for you. You'll have to pay for the software to have access to the full functionality.
But you can try this little trick using autodock4
1) load your cleaned protein (after removing all water molecules and heteroatoms)
2) go to edit 》 misc 》 check for missing atoms (this would tell you if the protein structure has missing atoms or not. If it does, proceed to number 3)
3) go to edit 》 hydrogen 》 add hydrogen 》 add pollar hydrogen only.
4) go to edit 》 misc 》 check for missing atoms.
If you follow the process duly, you shouldn't see any missing atoms in the panel again.
This process is right because all X-ray crystallography structures lack polar hydrogen atoms and this is one of the major reasons protein structures have missing atoms.
Abdeen Tunde Ogunlana, I was checking for missing atoms before adding the polar hydrogens, i'm going to try do it after then. Hopefully it will work! Thank you!
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