[phenixbb] Bad ligand parameters
Joe Krahn
krahn at niehs.nih.gov
Mon Sep 28 11:45:42 PDT 2009
I found that residue TRS has different dihedral target angles for the
three hydroxyl oxygens, which are actually all equivalent. They have a
periodicity of 1, but should have a periodicity of 3. What is the best
way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference
structure, and there is probably a lot of conformation bias. In this
case, it seems that parameterization should have been able to detect
symmetry. It would be nice if parameters could include information about
whether a human has done any validation. Actually, a ligand Wiki might
be nice, where people can easily put comments, even if they are not sure
about how to improve the parameters.
Joe Krahn
More information about the phenixbb
mailing list