Dear colleagues, I have some doubts about molecular docking, and I would like to know if you could guide me based on the experience you have.

I use Molegro Virtual docker (MVD) software, which only works with .mol2 format. However, prior to the selection of my compounds, I perform a virtual screening. Nevertheless, I continue having 250 molecules (from ChEMBL) to analyze. My problem is that, to download these molecules, I download them via their ID from the pubchem platform in .sdf format and then verify their structure in alvamolecule.

My problem is that at the moment of loading them to MVD, due to the .sdf format, it does not detect that the ligands have any partial charge assigned to them. My first option to solve this was to transform with other software the compounds from .sdf to .mol2, I did it and it still does not detect loads. The option that worked for me is to get the 3D structure from the name of each compound using avogadro and saving in .mol2 format. The problem is that I find it impractical when you have a large number of compounds to screen. Do you know of any other way how it can be done? Or any material I can read to guide me in these doubts? Finally, if a batch docking is performed (with the same parameters) to reduce the computational demand, is it correct to do it this way? Or is it better in a single run to perform all the analysis of these compounds. Thank you very much