[phenixbb] Bad ligand parameters
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.
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