I'm trying to perform a docking experiment using the GOLD software. To do so, I initially prepared my ligand in CHIMERA, added hydrogens and charges (protonation state +3). However, after running my first docking round in GOLD, some hydrogens were not recognized and were labeled as ****. What could be causing this issue? What might have gone wrong?
Note: I also tried minimizing the ligand using OpenBabel, but the same issue persists.
If you are sure that these were hydrogen atoms, probably something has gone wrong during switching between different format files. Perhaps Chimera gave some hydrogen atoms some strange names, that Gold did not recognize? You can manually edit the input file to Gold (or the saved file from Chimera) and perhaps change the naming of these hydrogen atoms (I'm not sure which format is Gold using - PDB?).
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