Re: [Apbs-users] huge standard deviations
Biomolecular electrostatics software
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From: Nathan B. <ba...@bi...> - 2009-08-07 16:22:29
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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... > Skype: dimitris3.16 > > > > > > > > 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 >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports >> 2008 30-Day >> trial. Simplify your report design, integration and deployment - >> and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july_______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users > > — > 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/ > > > > > > > > > > > > > > — 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/ |