How to set up the requirements for covalent docking using AutoDock4?

12 October 2022 3 9K Report

Hi everyone! I tried to do covalent docking using the scripts available on the AutoDock4 website, and it is said that I need python and openbabel python bindings. I installed python on Linux and then openbabel using the source code (http://openbabel.org/wiki/Category:Installation).

I unpacked the downloaded openbabel folder in my home directory. I opened the folder, and in the terminal I wrote the line of commands being in the openbabel folder:

mkdir build

cd build

cmake .. -DPYTHON_BINDINGS=ON

make -j4

make install

In the end, I got the message that open babel 3.1.1.1 is installed.

Then I tried to align my ligand and protein with this line:

python ~/local/adcovalent/prepareCovalent.py --ligand ligand.mol2 --ligindices 1,2 --receptor 3upo_protein.pdb --residue B:SER222 --outputfile ligcovalent.pdb

but I got an error message:

No module named pybel was found.

I tried several things I found on the web, but nothing was helpful, pybel just could not be found. Has anyone encountered the same problem, and could you explain to me step-by-step how did you overcome it?

Regards,

Ljubica

Mohamed AbdElAziz Khamis Omar

Article Covalent Docking using Autodock: Two-Point Attractor and Fle...

Article AutoDock4 and AutoDockTools4: Automated Docking with Selecti...

https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf

Ljubica Brenjo

Dear Mohamed,

I have already read all the articles and the tutorial, but they do not explain this kind of issue. For the covalent docking, they added a readme.txt file that explains that there are two requirements before docking:

REQUIREMENTS

- Python >=2.6

- OpenBabel Python bindings

(On Debian/Ubuntu derivatives, it can be installed with "apt-get install python-openbabel")

- Basic experience with docking with AutoDock

I have installed python and I also installed openbabel as described in my question. Openbabel could not be installed like they explained with the simple command: sudo apt-get install python-openbabel

so I compiled it from the source as already explained. But when I tried to align my ligand and protein as they explain, the warning "No module named pybel" is always returning. I could not find the answer in neither of the suggested material.

Adnan Majeed

visit this

Article Covalent Docking using Autodock: Two-Point Attractor and Fle...

https://autodock.scripps.edu/resources/covalent-docking/

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