[phenixbb] Bad ligand parameters
Nigel W Moriarty
NWMoriarty at lbl.gov
Mon Sep 28 12:09:48 PDT 2009
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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> 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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