Tao

Thank you so much for taking the time to answer our questions.

Hi, would you mind providing the link to the script you posted? In order to answer the questions we discussed, I would like to have a look at it.

Dear Koes, I can understand what him/her was asking. Because I have the same question recently when I try to do structure-based virtual screening using smina. In the tutorial, smina runs with receptor.pdb and combined_ligand.sdf. The problem is autodock4 would prefer using pdbqt format input for it is protonated and added hydrogen. In addition, some believe that protonated ligands and receptors could dock more precisely and results could be more confident. Our questions are: Does smina run with unprotonated...