The standard deviations are overestimates since it assumes no correlation
between the different terms when the difference is taken (it uses the
standard propagation of errors technique). This will likely be changed in
future versions to take the standard deviation of a difference population
(that way you will get a standard deviation closer to what you expect --
that is ~0 for non-interacting residues) if I can find a memory-efficient
way of doing it (however, storing arrays for each residue pair for each
snapshot for the complex, receptor, ligand, and differences can quickly
consume 10s of GB of physical memory for lots of frames for large systems,
which is why the present implementation was opted for).
However, like Dave pointed out, there's nothing wrong in principle with the
given data characteristics.
HTH,
Jason
On Mon, Aug 8, 2011 at 3:50 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Hello All
>
> I am calulating per residue free energy decomposition of protein-DNA
> complex.
> Result I have got having standard deviation larger than average value. For
> examplex backbone energy for GLN 78 :
>
> Residue | Location | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
> GLN 78 | L GLN 49 | 0.000 +/- 2.640 | -0.241 +/- 0.806 | 7.188
> +/-
> 2.331 | -7.194 +/- 1.172 | 0.000 +/- 0.000 | -0.247 +/- 3.799
>
> How I should interprate this result.Will it be relaible for furter
> interpratation?
>
> Anyone please suggest me.
>
> With regards
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Aug 08 2011 - 06:30:04 PDT
