Hello Lisa--

> I'm attempting to refine a structure against ATCUN PRE R2 relaxation
> data, but am hitting some errors.  
> We've successfully added the ATCUN motif to the protein using the
> eginput/PSF_generation/tags/atcun_motif/addATCUN.py script 
> We've modified an ensemble script (with eefx now working, thank
> you), starting from the newly generated ATCUN-protein.pdb and adding
> the prePot potential 

My colleague Guillermo Bermejo pointed out to be that you must be
careful using actun top/par values with eefx- they are not 
compatible. Things may work but there are no guarantees.

> rampedParams.append( StaticRamp(setupSBMFmode( pre )) )
> highTempParams.append( StaticRamp(setupSBmode( pre )) )

I think you'll want SBmode throughout, at least initially.

> ---
> This will run fine (if not doing a great job satisfying the PRE data), but is 
> giving an error during writeStructure:
> "Error calculating structure 0: 'PREPot' object has no attribute '__getitem__'
> Warning: fitting EnsembleSimulation structures"
> The bottom of the output file:
> ensemble-atcun.py(384):     loopInfo.writeStructure(potList)
> Traceback (most recent call last):

This is a simple bug, which is corrected in the attached version of
prePotTools.py which should be placed in the python subdirectory of
your Xplor-NIH 2.43 distribution.

> So - do we need to explicitly include the atcun.par file in our
> refine runs as is done int he addATCUN.py? Or is the error coming
> from something else?  

You should include atcun.par, but all bets are off when used with
eefx. You might try with standard top/par values first.

best regards--

Attachment: prePotTools.py
Description: Binary data

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