[phenixbb] Bad ligand parameters
Joe Krahn
krahn at niehs.nih.gov
Mon Sep 28 13:43:33 PDT 2009
Nigel,
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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
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