[phenixbb] Bad ligand parameters
Nigel W Moriarty
NWMoriarty at lbl.gov
Mon Sep 28 13:56:32 PDT 2009
Joe
It is in the nightly builds if you are inclined. You are also free to
download the restraints from the GeoStd open source project.
Nigel
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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