[phenixbb] Bad ligand parameters

Nigel W Moriarty NWMoriarty at lbl.gov
Mon Sep 28 16:34:18 PDT 2009


I guess you are correct.  I'll have a closer look.


On 9/28/09 4:18 PM, Joe Krahn wrote:
> GeoStd seems not to have an files. Is it only available via SVN for now?
> The GeoStd parameters still need some work. The equivalent hydroxyls are 
> not symmetric. One of the dihedrals has a base angle of -175.0 instead 
> of 180 (or +/-60). One has an esd of 30.0, and the others have an esd of 
> 20.0. The hydrogen ESDs also seem a bit too tight, and probably should 
> have a periodicity of 3.
> They are an improvement, but I don't think automated parameterization 
> will ever be perfect.
> Joe
> Nigel W Moriarty wrote:
>> 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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090928/10064b23/attachment-0003.htm>

More information about the phenixbb mailing list