Hi everyone,

I am trying to prepare 321 ligand molecules for further molecular docking process. Ligand preparation consists of 3 steps as (i) adding hydrogen atoms (ii) adding partial charge by gasteiger (iii) separating sdf file including 321 molecules into individual 321 sdf files (just like 1.sdf, 2.sdf, 3.sdf and so on). Afterwards I apply UFF minimization and convert sdf files into pdbqt files. However, what I see is always loss of hydrogen and double bonds. I could not find any solution for this and I am stucked... If anybody has an advice or solution about the situtaton, I would be very happy for sharing information....