[phenixbb] Bad ligand parameters

Joe Krahn krahn at niehs.nih.gov
Mon Sep 28 13:43:33 PDT 2009

I am using PHENIX 1.4-6, which is newer that the most recent version on 
the PHENIX web site, other than "nightly build" versions.

Nigel W Moriarty wrote:
> Joe
> 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 
> http://sourceforge.net/projects/geostd
> Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
> Nigel
> 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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