Re: [Apbs-users] huge standard deviations

[Nathan B. <ba...@bi...>]

Hello --

> Thank you very much for your answer!
> Indeed, even though my system is pretty small (66 aminoacids the  
> protein and 10 aminoacids the ligand) I observe that the alpha  
> carbon RMSD of the system is pretty high (0.2-0.8 nm in 1 ns). The  
> two highly mobile N-term and C-term protein ends (composed by polar  
> aminoacids, mostly) account for much of the RMSD.
> Is it possible that such a mobility generates the high standard  
> deviations?

Yes, definitely.

> If so, this does not seem to happen for the apolar solvation terms  
> too due to the nature of the aminoacids composing the ends?

The volume, area, and integral terms of the apolar energy definition  
are much less sensitive to conformational changes.

> I had thought that this extensive mobility could affect the  
> calculations, but I have come to a consideration. Let's divide the  
> mobility effects into two categories: the effects affecting the  
> interaction directly and those who don't. Since I perform the  
> subtraction "complex - protein - ligand", the latter effects should  
> cancel out.
> Is this hypothesis correct?

I'm not sure; I think this would be very system-specific...

-- Nathan

> Thank you very much in advance!!!
>
> d.
> _____________________________________
> Dulbecco Telethon Institute c/o DIBIT Scientific Institute
> Biomolecular NMR Laboratory, 1B4
> Via Olgettina 58, 20132 Milano (Italy)
> Tel     : 0039-0226434348/5622/3497/4922
> Fax    : 0039-0226434153
> Email : spi...@hs...; dim...@gm...
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> 2009/7/30 Nathan Baker <ba...@bi...>
> Hi Dimitrios --
>
> Such variance is fairly standard in polar solvation energies.  Part  
> of the "problem" is related to sensitivity in the sharp dielectric  
> boundary while part of the issue is related to the intrinsic  
> conformational sensitivity of polar solvation.  I'm not sure that  
> such variance really is all that surprising.  You could try a  
> smoother dielectric boundary (e.g., splines) but please be aware  
> that these require specialized parameters.
>
> Thanks,
>
> Nathan
>
> On Jul 29, 2009, at 10:12 AM, Dimitrios Spiliotopoulos wrote:
>
>>
>> Hello APBS users!
>>
>> I have a question about the standard deviations values of my  
>> simulation-derived structure files of a protein interacting with a  
>> peptide.
>>
>> I performed five simulations (each composed of 1 ns NVT  
>> equilibration and a 3 ns NPT production run) and pasted them  
>> together in order to get a single "overall" simulation. On this  
>> latter simulation, I performed the MM/PBSA calculations.
>> I noticed that the polar solvation contribution had standard  
>> deviations that are 1- to 3-fold the mean value (e.g., -36.8534 +/-  
>> 78.0839 kJ/mol or -88.9041 +/- 88.6444 kJ/mol), whereas my apolar  
>> solvation contribution has more reasonable results (the standard  
>> deviations are 3-5% of the mean values). I thought may be the  
>> conditions were too permissive and my simulation was oversampling,  
>> so I changed them into 100 ps NVT and 100 ps NPT. Thus, I  
>> calculated the values for all the frames (1000) or every 10 frames  
>> (100), but I had very similar results.
>>
>> I cannot figure out why the standard deviations of the polar  
>> solvation term are so high: is there any parameter in the polar  
>> solvation calculation input file that can affect this?
>>
>> Thank you very much in advance!
>>
>> Dimitrios Spiliotopoulos
>>
>> _________________________________________________________________________________________________
>> Dulbecco Telethon Institute c/o DIBIT Scientific Institute
>> Biomolecular NMR Laboratory, 1B4
>> Via Olgettina 58, 20132 Milano (Italy)
>> Tel     : 0039-0226434348/5622/3497/4922
>> Fax    : 0039-0226434153
>> Email : spi...@hs...; dim...@gm...
>> Skype: dimitris3.16
>>
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> —
> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
> Director, Computational and Molecular Biophysics Graduate Program
> Center for Computational Biology, Washington University in St. Louis
> Web: http://bakergroup.wustl.edu/
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—
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/