I’ve created a PDB file for a small molecule inhibitor that I docked with its protein partner. When the PDB file is opened in PyMOL before docking, it appears as it should but the outputted docking structure shows one of the methyl groups on the ring structure as a lone sphere rather than connected to the ring. Is this a visual issue or is the program actually disconnecting the atom? How can I remedy this issue?
Usually this is indeed a display issue.
And nonpolar hydrogens are removed by default in HADDOCK (can be turned off)