ADL: saving the docked structure

Steve Darnell sdarnell at oncology.wisc.edu
Wed Jan 21 11:45:30 PST 2009


Ishwar,

Personally, I use the python scripts for analyzing dockings (provided 
with ADT) to write a pdb file for the lowest energy conformation and the 
lowest energy conformation of the largest cluster.

http://autodock.scripps.edu/faqs-help/faq/where-can-i-find-the-python-scripts-for-preparing-and-analysing-autodock-dockings

Specifically, I use:

write_lowest_energy_ligand.py
write_largest_cluster_ligand.py
pdbqt_to_pdb.py

If these are not one of the conformations you are interested, you can 
also use "write_all_complexes.py" and find the one you are interested 
in.  Sorry, I have not used ADT long enough to know how to do it 
interactively.  Perhaps someone else has that answer.

Regards,
Steve

--
Steve Darnell
University of Wisconsin-Madison
Madison, WI USA


ishwar chandra wrote:
> Hi All;
> I would like to know how can we save the docked structure of protein &
> ligand after docking
> i tried to save it like this
> File-->Save-->Current Session(file format .pdb)
> so as to save it in pdb format & 2 c the structure where it has formed
> different bondings in pymol or chimera
> i am unable to open the saved structure in pymol as it shows nothing.
> Please reply soon if anyone knows. Thank you all
>  regards
> Ishwar
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