[phenixbb] Bad ligand parameters

Nigel W Moriarty NWMoriarty at lbl.gov
Mon Sep 28 12:09:48 PDT 2009


I think you may need to upgrade your version of PHENIX.  In the current 
version, the periodicity is 3.  I have recently been using eLBOW, the 
Chemical Components library and the Monomer Library to improve any 
residue restraints that have short comings.  These are freely available 
at Source Forge from a project called GeoStd at 

Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd


On 9/28/09 11:45 AM, Joe Krahn wrote:
> 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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> phenixbb at phenix-online.org
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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