[RASMB] SEDANAL - Issue with Claverie Simulations and Numerically Stable Fits

Walter Stafford wstafford3 at walterstafford.com
Thu Mar 1 08:07:23 PST 2018


Hi Richard,
The first thing I would do is increase the number of points to 1000 or even 1500 pts. ... or higher if that doesn't work
The Grid Check message appears if the gradients are too steep at the base (or the meniscus.) 

What are the molar masses of the species in your model? This can become a problem for molecules above 150 kg/mol.

If you send me a package, I'd be happy to take look at it.

It sounds like you'll have to add an incompetent species to your model - easy to do with the Model Editor.

Give me a call if you want. 978-886-5267

Walter Stafford
wstafford3 at walterstafford.com

Love all, trust a few, do wrong to none. 
- William Shakespeare
   All’s Well that Ends Well,  Act I. Scene I.


> On Feb 28, 2018, at 11:36, Richard Itwaru <richard.itwaru at regeneron.com> wrote:
> 
> Good morning all!  I’m a relatively new user of SEDANAL (v6.67) and I’m trying to extract some kinetic data from a model system. 
>  
> I’m trying to fit 6 sets of absorbance data of Protein A and Protein B to a 1-1 binding model.  This is a fairly heterogenous system, where there are sites for up to a 6:1 complex of proteins. 2D distributions show a fair bit of heterogeneity (both by s- and f/f0), but the distribution shows that the majority complex is 1-1 by c(s), with some incompetent Protein A.  I want to use this 1-1 model as a first guess for parameter estimation.    I know the kinetic off-rate is fairly fast (>0.00001 1/s), but in my attempts to fit for this parameter, I run into trouble.  I find that my Claverie simulations are not robust enough to generate good fits.  I either end up with the fit crashing, or end up having to force the finite-element simulations to continue with negative concentrations and end up with “CHECK GRID” errors. 
>  
> How can I generate better, more stable models?  I understand that CHECK GRID has to do with coarseness of the simulation grid, where I’ve tried 200 and 400 points. Should I try to increase the number of points even more? For reference, I’m using Newton-Raphson at the initial equilibrium to fit.  I’m hoping this non-analytical algorithm can help to calculate and redistribute the loading concentration of Protein A into its competent and incompetent forms.  Should I instead add another component to my model, Protien A’, that is non-interacting?  My simulation then moves on to  SEulEx for equilibration during run and ends with Newton-Raphson again.
>  
> Thanks for your help in this matter.  At this point, I’ve run my head into the wall!
>  
> Richard Itwaru
> Research Associate II – Protein Biochemistry
> Regeneron Pharmaceuticals
> Work: 914 – 847-3594
> Email: Richard.itwaru at regeneron <mailto:Richard.itwaru at regeneron>.com
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