[phenixbb] Bad ligand parameters

Nigel W Moriarty NWMoriarty at lbl.gov
Mon Sep 28 13:56:32 PDT 2009


It is in the nightly builds if you are inclined.  You are also free to 
download the restraints from the GeoStd open source project.


On 9/28/09 1:43 PM, Joe Krahn wrote:
> 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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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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