Hi Friends
I want to dock a ligand which binds covalently to the protein active site (Cysteine).
I have used auto dock scripts which were provided in the link http://autodock.scripps.edu/resources/covalentdocking
I have followed as it is in the README text
But I'm getting the following error
[user@mqml Desktop]$ python /usr/local/bin/adCovalentDockResidue/adcovalent/prepareCovalent.py --ligand ligand.mol2\
> --ligandindices 1,2\
> --receptor 3upo_protein.pdb\
> --residue B:SER222\
> --outputfile ligcovalent.pdb
Traceback (most recent call last):
File "/usr/local/bin/adCovalentDockResidue/adcovalent/prepareCovalent.py", line 36, in
import pybel.py
File "/usr/local/bin/adCovalentDockResidue/adcovalent/pybel.py", line 16, in
import openbabel as ob
File "/usr/local/bin/adCovalentDockResidue/adcovalent/openbabel.py", line 37, in
_openbabel = swig_import_helper()
File "/usr/local/bin/adCovalentDockResidue/adcovalent/openbabel.py", line 29, in swig_import_helper
import _openbabel
ImportError: No module named _openbabel
Can anyone help me how to rectify this?
Hi,
Autodock is widely used molecular docking software, applies two methods to covalently dock inhibitors to receptor: a “grid-based method” and a “modification of the flexible side chain” approach. In flexible side chain, the covalent bound ligand and the protein attachment are treated as a single flexible side chain and sampled as part of the receptor. The grid-based method, utilizes a Gaussian biasing function with is centered on the protein attachment atom and also the grid-based energy to bias the covalent bonding ligand pose. However, the application of a covalent docking feature requires manual definition of the reactive atoms and reaction type as well as manual preparation of the ligand and protein structure files, leading to difficulties in up-scaling the process for screening purposes. Another program called CovalentDock has addressed this problem by automatic preparation of ligand files but is limited in reactions. For more details, please go through the attachment.
"ImportError: No module named _openbabel"
---
The OpenBabel Python bindings are not properly installed.
Dear Martin,
I had similar issue in past. Till now I could not import pybel or openbabel from Python or command prompt in windows 7. How this could be done?
Rajesh
Following the instructions . . .
https://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html
---
1. Install OpenBabelGUI.
2. Install OpenBabel Python bindings.
---
It works with 32-bit versions of Python only.
Even I was facing this same problem. Had to install openbabel first, and then change the import pybel line to from openbabel import pybel
Also, the python2 version does not work now. It has to be converted to python3 with the 2to3 command.
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