Swig/python BHtree memory leak in autodock 4: how can I solve it?

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

Hi, . 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.

, 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!

Dear scientists,

I am having the same problem. Can anyone tell me how to correct it? I tried a few times and it is still the same. Thank you very much!

Hi, Ly Duyen

I've looked exhaustively over the internet about this problem, but never found anything that could solve it. Looks like memory leaks are commom in python. What I did was run the dockings I wanted in another computer that did not show that error and the results were the same. So, I presumed the error was not having an impact on the reliability of my results. I'm also using windows, as well as everyone that messaged me about the same problem. I guess this is a windows-related problem.

Thank you very much professor! Julio Thurler

Hmm... I think I'll try working on a Macbook to see if there's a better result.

I've searched all over the web but no one has been able to answer this problem yet.

I'm doing this research for my graduation thesis, so I'm still worried about overcoming this problem to get the expected results.

Hello everyone. Did anyone get it solved? I am facing the same problem.

Hello Everyone,

I am having the same memory problem. Interestingly, I was able to use the program one and a half months ago without any errors, now the program throws me the very same memory problem. I installed an older version of Anaconda and Python (2019 release, Python 2.7) and I re-installed MGLTools and tried once more. Thrown me the same error. I upgraded Vina to the current version and re-installed the Python script I'm having problem with manually. It is prepare_ligand4.py. I have no idea why it is happening. I am running the programs on Windows 10. All the help is very much appreciated. Thank you so much beforehand.

Hello Again,

After doing all of those above, interestingly, the program has provided good enough .pdbqt output for Vina. Vina worked well with the new .pdbqt. Just wanted to note that. By the way, I use MGLTools1.5.7. Hope everyone's problems were sorted out.

Hi guys, I am also having the same problem with the appearance of that error. I would like to know if it affects the final results. In my case, I am using Windows 11, and i have reinstalled all current versions of all the required tools, but it keeps giving me the same error: ''swig/python detected a memory leak of type 'BHtree *', no destructor found''.

As a result, the final command stage of Autodock vina always runs into errors, and i fail to obtain the needed docking structures of my protein-ligand interactions

Aboagye Kwarteng Dofuor This looks like a commom problem of people using Autodock on windows. I've tried running the same docking, with the same experimental conditions on other computer and it gave me the same results. So I assumed the error was not making a difference in the docking run.

I agree, the memory leak warning does not make a difference. The docking works fine.