Thomas Evangelidis

Hi David, Thank you for the clarifications. What is the recommended way to go? Can I safely use the multi-molecule SDF as input in just one dockign run? If not, how to safely convert SDF to PDBQT, with 'prepare_ligand4.py" from AutoDock Tools? I currently do that with OpenBabel. Best, Thomas

I am really troubled by the output of Smina. One of the its greatest advantages over Vina was that there is no need to convert to PDBQT, Smina can read in a multi-mol SDF file for example and dock every compound onto the receptor. Below I demonstrate that: the docking poses and energies obtain from SDF input are different than from PDBQT input although I use the same --seed and parameter values. the protonations of the output files are also different, although I use '--addH off' to prevent the code...