Open stefdoerr opened 2 years ago
Are there any updates on this?
@stefdoerr -- are you able to share the patches you mentioned above? Thanks.
https://github.com/Acellera/moleculekit/blob/main/moleculekit/tools/preparation.py#L475-L491 It's a bit specific to my library though. But the main idea is simply to check some residues if they have atoms which correspond to a specific protonation and if that's the case, rename them to that protonation state.
Running on PDB ID 1UNC of Villin https://www.rcsb.org/structure/1unc causes the following crash The issue is that the residue is named GLU but it has a HE2 hydrogen which corresponds to a GLH residue. Then pdb2pqr crashes because it's GLU template doesn't have a bond to any HE2 hydrogens. Do you have any plans on fixing this? In the meanwhile I will make my own patches but just wanted to point out the issue.