[phenixbb] dihedral error

Pavel Afonine pafonine at lbl.gov
Thu Aug 7 08:30:24 PDT 2008


Hi Simon,

did you try to use eLBOW to generate a cif file? If you use PHENIX, then 
using eLBOW is an obvious choice to create cif files for your ligands:

phenix.elbow model.pdb --residue=XXX

or

phenix.elbow model.pdb --do-all

Pavel.


On 8/7/2008 7:40 AM, Simon Kolstoe wrote:
> phenix.refine keeps on stopping with the error:
>
> AssertionError: Conflicting dihedral restraints:
>    tor id: var_002
>    1. definition from: residue: DRG, conformer A
>    2. definition from: residue: DRG, conformer A
>    atoms:
>      " CB  DRG A 500 "
>      " OG1 DRG A 500 "
>      " PAL DRG A 500 "
>      " OAF DRG A 500 "
>
> It is for a phospho-threonine residue whose dictionary I made in  
> PRODRG. I've tried all the different charge states of the phosphate  
> however phenix gives the same error every time. Any ideas?
>
> Thanks,
>
> Simon
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