Thanks Jason and Dave for my clarification.
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Aug 08 2011 - 09:30:02 PDT
