Non-converging Runs

[Leah Roe]

Hi all, 

I'm new to Ponderosa and was just playing around with it a little bit today. I had a run complete with a fairly standard setup (screenshot attached). In Analyzer, it looks to me that the result doesn't converge since there are not multiple structures and the overall score is quite high (~5049) - screenshot attached. The protein is 167 amino acids, I was wondering what most people to do improve non-coverging runs? Do you try a different calculation option or # CPUs, etc.  Or if this is a different problem entirely? 

Thanks!

Leah

[Leah Roe]

One more follow up question, is there a reference for what values I should be expecting for what a "good" run looks like, and what all the analysis parameters mean?

Thanks! Sorry, still just getting started, help appreciated. 

Leah

[Lee, Woonghee]

Leah, first thing is to make sure you have full, reliable assignments and peak list files contain sufficient peaks. Then, you can provide partially assigned NOE peaks when you run PONDEROSA. Also, you can provide close contact information (.wlt) for known neighboring residues for guidance. Tolerances can be considered to be adjusted based on spectral consistency between your chemical shifts and NOESY, too. This should be done iteratively.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Visiting Assistant Professor (Aug. 2020)

       and

Assistant Professor (Sep. 2020 - )

 

Department of Chemistry

Campus Box 194, PO Box 173364

University of Colorado Denver

Denver, CO USA 80217-3364

woongh...@ucdenver.edu

https://sites.google.com/view/wlee-group 

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