I am using PyRx interface for running AutoDock 4.2 After docking I get .dlg files as usual. now i wish to create complexes of poses obtained from dlg file.
There are these two python scripts to get this job done. (to extract the docked configurations from dlg file using the script "write_all_complex.py" can be used. This script will write the ligand - receptor complex coordinates into pdbqt format. subsequently, "pdbqt_to_pdb.py" script can be used to convert the pdbqt files into pdb.) But these scripts are known to run via ADT (Not through PyRx).
So my question is that is it possible to run these scripts independently (like using python GUI like IDLE) and obtain results without using ADT.
I would be grateful if some one provide me with these two scripts since i am not using ADT. Or is there any other easy means to generate complex of poses obtained in dlg file and protein used as target in docking run.
For ADT user all the scripts I need are located in folder ~ /MGLTools-1.5.X/MGLToolsPckgs/AutoDockTools/Utilities24/
where all other python codes are available
Hello,
I was also looking for the same and I came across a script provided by NBRC called BINANA. Its a python script which needs receptor.pdbqt and ligand.pdbqut (chose ligand conformation of your interest from dlg and get output to pdbqt ) and run command. Keep the hydrogendond cutoff 3.0 A for better analysis
Hope this helps you.
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