Hi, First thing is that "Autodock Vina" is different than "Autodock", i.e., they are two different programs. The docking program "Autodock" uses charges, so the options may have some effect. It is unlikely that your input has lone pairs, so it's probably the hydrogens option making a difference. The docking program "Autodock Vina" does not use charges, so as far as I know, the options should not have any effect. If you are using Autodock Vina, I don't know why the results would be any different. However, we are not the developers of Autodock or Autodock Vina, so if you want to get into more details about those programs, take a look at their websites: Autodock Vina <https://vina.scripps.edu/> Autodock <https://autodock.scripps.edu/> Just from your description, however, you could just always use both of the merging options turned on. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 11, 2024, at 7:21 PM, via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges

Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with)

While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it.

My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings.

Any insights into this matter is highly appreciated.

TIA