Converting PDBQT output to PDB in VINA

Question

[marawanhussain]

Dear Biostars Stars,

I am trying to use VINA for high-throughput screening followed by MD simulation. I am struggling to find a good way to convert the protein-ligand PDBQT complex to a normal PDB file again to use for MD in AMBER. As you know the PDBQT file has no hydrogens on the ligand, except polar hydrogens. The main issue comes from the inability of the command line tools to do this conversion correctly, such as do proper connection and/or add Hydrogens especially for the ligand. I am asking if someone knows a good way/script to do that correctly. openbabel or MGtools do not work.

Regards,
Marawan

[kanika.151]

Hello,

You can use AutoDock Vina to interchange between PDBQT to PDB.

Also, you can use just AutoDock to remove hydrogens and save it in PDB format and then use it in AMBER.

This can also be done by using Discovery Studio.

Answer 1

[db4]

They are commands here to convert to pdb.

[Ricard]

The link posted in this answer is broken, does anyone know a command-based way to perform this conversion?