Hi Jason,
Thanks for your reply!
But I am not able to figure it out how should I input my output to pymbar.
where can I find this mdout2pymbar.pl script??
thanks
On Wed, Jul 31, 2013 at 10:21 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Jul 31, 2013 at 1:07 PM, Kumar Sonu
> <sonu.bioinformatics.gmail.com>wrote:
>
> > Hi,
> >
> > I have done TI using 5 point gaussian quadrature lambda values for my
> > calculations. Now I am facing problem in calculating error along with
> > binding energy. Is there way to calculate error??
> >
> > for binding energy, I am multiplying corresponding weight of each point
> > with Avg. dV/dL value and finally summing up for total energy. But I have
> > no idea to estimate error?
> >
>
> You can measure the statistical uncertainty of the measurement using MBAR,
> an analysis that's even supported by sander's TI module (see the ifmbar
> variable in sander and the mdout2pymbar.pl script that postprocesses the
> resulting mdout file).
>
> If you google "pymbar" you should be able to find the pymbar implementation
> from Shirts and Chodera (it's worth reading their paper, too).
>
> You may be able to get a general idea of the size of the error by
> bootstrapping the DV/DL values you pull from the mdout files N times and
> computing the free energy for each bootstrapped subsample. Then you can
> take the standard deviation of your N subsamples as a (overly?)
> quick-and-dirty estimate of your statistical uncertainty (note, MBAR is far
> more rigorous in this regard).
>
> In each case, the data must be uncorrelated, or your uncertainty estimate
> will be meaningless.
>
> Other errors, like force field and sampling errors, are far harder to
> quantify.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
-------------------------
Sonu Kumar
Postdoctoral Associate
Infectious and Inflammatory Disease Center
Bioinformatics and System Biology
Sanford-Burnham Medical Research Institute
10901 North Torrey pines Rd
La Jolla, CA 92037
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Received on Wed Jul 31 2013 - 15:00:02 PDT
