[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

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