Why hydrogen atoms are not included in resulting SDF files?
In the current version of eHiTS, we are not outputting the protonation state that we are using in the scoring. The way we sample protonation is by using a local model only, no consideration for pH at all. If a location can be protonated or de-protonated, we score it as if it were either, then choose the protonation state that scores the best. Essentially, for a given pose we are giving it the “best score possible”. There are several problems when outputting the protonation states. One is that a protonation state is a property of the complex not just the ligand, therefore we would need to have the corresponding receptor information as well. We are working on incorporating this in CheVi (we will show both the receptor and ligand protonation). The second, is that as you change protonation, tautomers could also change, and we currently do not have a mechanism of fixing the tautomers. We are currently finishing up a project to address this issue, and it should be in the next release. So wha
