By this reference, there isn't much explicit bond order information left in the .pdbqt if you transition from .sdf to .pdb. With the all-lowercase SMILES string c1ncncn1 for triazine, the explicit atoms are considered as aromatic, too. — Buttonwood Sep 2 at 13:23

Equally noteworthy is that these two models are both incomplete (no hydrogen atom at all) and flat 2D. Except for the triazine ring e.g., in the first model, this may hinder further work. — Buttonwood Sep 2 at 13:32

Thank you for your answer!. I also added the hydrogens before the sdf to pdbqt transition by several methods including seeSAR and/or OpenBabel. The conversion to 3D did not affeted the double bond conections either. Any other ideas? — Julio Coll Sep 2 at 17:51

Thank you very much Buttonwood ! — Julio Coll Sep 3 at 7:29

I am using obgui in windows, can that be the problem? Can I change any of the code at ob ? I am finding the same problems with unique sdf but my plans are to screen for thousands of Tirazine pdbqts!!! I will continue exploring your suggestions Thanks again!. I tested you final pdbqt by AutoDock Vina. Visualizing the pdbqt saving it as sdf again misplaced the double bonds at the Triazine.... — Julio Coll Sep 3 at 8:23

The commands e.g., in the manual's section of examples should not depend on the operating system, and thus equally act in cmd.exe of Windows. I note, despite using -h in the CLI (as recommended here to retain hydrogens), only H of OH are retained in version 3.1.1. obgui removes the other H present in the .sdf if writing .pdbqt, too. Is this expected? May .pdb retaining H an alternative for you? — Buttonwood Sep 3 at 14:19

The tutorial of autodoc vina here, around 4:25 min:sec shows that .pdb equally may be imported (OpenBabel would offer to write them with H (obabel -isdf input.sdf -h --gen3d -opdb -O output.pdb)) and later states polar H (like OH) were a requirement for the program to AutoDock Vina to work. (9:40 min:sec is noteworthy, too.) Maybe this is why openbabel removed almost all hydrogens from .pdbqt in first place. If you want to process thousands of files, however, the command line instructions likely will outperform the approach by mouse clicks and GUI. — Buttonwood Sep 3 at 14:33

thank you again but those suggestions did not solve the problem with pdbqts. Double bonds disappeared in Jmol when I visualized the pdbqts that you sent to me. I reproduced your steps and got the same result. pdbqt files just omitted any double bonds representation even when those were clearly stated in their texts! — Julio Coll 2 days ago

As mentioned yesterday pointing to this reference or now one by scripps.edu, .pdbqt does not discern between single, double, aromatic, or triple bonds; in this file format, atoms either are connected with each other, or not. However, .pdb (which the video shows once in the file manager to open input files) may retain this information (equally for Jmol./Support_for_bond_orders). — Buttonwood 2 days ago

My concerns started when the same input .sdf files were docked to seeSAR (BioSolveIT) and to Vina. SeeSAR docked them with thousand-fold lower binding-scores!. Of course that could be due to different algorythms. However, I wonder whether AutoDockVina's deformates the sdf input structural information (i.e., no double bonds). When I redocked the Vina's .out_ pdbqt by seeSAR, their seeSAR binding-scores increased. In other words, How reliable is AutoDockVina's docking if their .pdbqt do not take into account some of the bonds? Or Do they? — Julio Coll 2 days ago