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