[phenixbb] dihedral error

Simon Kolstoe s.kolstoe at ucl.ac.uk
Thu Aug 7 09:36:45 PDT 2008


Thanks everyone.

I had already tried the hiccup TPO file which hadn't worked either,  
but elbow seems to work well.

Simon



On 7 Aug 2008, at 16:30, Pavel Afonine wrote:

> 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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>>
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