ADL: pdbqt to pdb

Stefano Forli forli at scripps.edu
Wed Jan 24 10:23:36 PST 2018


Hi,

You can do it in different ways, either using the ADT graphical interface or by using a 
dedicated script which is in your ADT installation:

pythonsh $MGLROOT/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py

pythonsh pdbqt_to_pdb.py
pdbqt_to_pdb: pdbqt_filename must be specified.
Usage: pdbqt_to_pdb.py -s filename

     Description of command...
         [-f]    pdbqt_filename
     Optional parameters:
         [-o]    alternative pdb_filename
         [-v]    verbose output


Hope this helps.

S


On 01/24/2018 09:17 AM, Waldo Acevedo Castillo wrote:
> Hello,
> 
> ​Open the pdbqt file with Autodoock Tools and save it as pdb
> 
> Regards,​
> 
> 
> El El mié, 24 de ene. de 2018 a las 13:08, Sundar <jubilantsundar at gmail.com>
> escribió:
> 
>> Hi everyone,
>>
>> What is the best way to convert pdbqt to pdb?
>> I used openbabel to do this. It worked mostly fine but with a few
>> compounds, specially with the ones have protonated Nitrogen, gets
>> destroyed.
>>
>> Thanks,
>> Jubilant
>> ________________________________________________
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>>
> ________________________________________________
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> 

-- 

  Stefano Forli, PhD

  Assistant Professor
  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  The Scripps Research Institute
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