I was looking at using the vmd ff-toolkit to optimize that topology of a drug, but I see that it needs the psf of the ligand without hydrogens because the ff-toolkit program puts water on it. In the cgenff server it did not run well (unfulfilled valence in aromatic subgraph; skipped molecule) and in the charmm -gui, the order of the atoms of the pdb is changed and the values on the right remain the same. How could you get the psf out of a ligand pdb ? I still can't get an initial topology for this ligand.

Previously, I have used openbabel to add hydrogens, then generating mol2 and str file, but I believe I must not this step for ff-toolkit.

Furthermore, the ff-toolkit use Molefacture to create psf and pdb, but I already have the pdb of protein data bank.

Please, could someone help me?

I attached my pdb file.