ADL: saving the docked structure

George Tzotzos gtzotzos at mac.com
Thu Jan 29 14:40:18 PST 2009


Hi Steve

Is the ligand saved in the protonated or unprotonated form? The  
complex.pdbqt file rendered shows the protein in the protonated form  
and the ligand unprotonated (in my case). Is this to be expected?

Cheers

George

On Jan 21, 2009, at 8:45 PM, Steve Darnell wrote:

> 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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