I need to up lode the protein ligand complex in pdb format for finding the binding parameters.
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
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
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.
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.
- Badges
- Science topic
- Similar topics
- Filing