babel -ipdbqt 'filename.pdbqt' -opdb 'filename.pdb'

use this in linux

Hi Sanjukta,

Check out the following links:

"Is there a way to save a protein-ligand complex as a PDB file in AutoDock?"

http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock

"Analysing Results"

http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Analysing%20Results

Or try Open Babel, which can convert various structural file formats:

http://openbabel.org/wiki/Main_Page

Hi, you can convert your pdbqt file to pdb by OpenBabel software

In autodock vina you can generate the results in .pdb format instead of .pdbwt

When you specify the name of outfile in the config file, name the output as output.pdb instead of output.pdbqt (or any other name you prefer).

Sanjukta Badhei please go through the link given below: http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html

Hi sajukta

There is python script in autodock installation folder pdbqt_to_pdb.py

You can use this script to convert the files easily using one line command

Search the file by adding prefix locate it will show u the exact location of python script

You can used Open Babel software

Totally agree with Rajeev

Using Auto dock vina you can easily convert pdb file into pdbqt. You can also use Open Babel software for the same.

babel -ipdbqt 'filename.pdbqt' -opdb 'filename.pdb'

use this in linux

http://openbabel.org/wiki/Main_Page

Open pdbqt file in Autodocktools and write pdb.

Autodock tools easily converts PDBQT to PDB and vice versa.

Load PDBQT file then file>save> write PDB. Choose the location to save the file.