Re: [Apbs-users] RE: Very Similar Binding Energies - Error Estimation
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Re: [Apbs-users] RE: Very Similar Binding Energies - Error Estimation
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From: Nathan B. <na...@at...> - 2004-09-17 08:55:24
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That certainly seems outside the range of error I'd expact due to numerical considerations. If too coarse a grid is chosen, than one might expect ~10% error in energy with respect to the “converged” calculations. There might be something wrong with your calculations; you should also make sure you are using the latest (possibly even CVS version) of APBS. Thanks & good luck, Nathan -----Original Message----- From: "Diego Vallejo" <va...@if...> Date: Thu, 16 Sep 2004 13:03:07 To:<ba...@bi...> Cc:<apb...@ch...> Subject: [Apbs-users] RE: Very Similar Binding Energies - Error Estimation Nathan, do you have, roughly, an error estimation of this Binding Energy calculations? I get -300 kJ/mol and I think this figure could be excessive.... Diego Vallejo > -----Mensaje original----- > De: Nathan Baker [mailto:ba...@bi...] > Enviado el: Miércoles, 07 de Abril de 2004 09:39 a.m. > Para: va...@if... > CC: Nathan Baker > Asunto: RE: Very Similar Binding Energies > > > What you outline below is the correct way to calculate the change in > solvation energy. I'm guessing this desolvation term will be greater for > the more highly charged molecule and may be the reason the net binding > energies are very similar... > > -- > Nathan A. Baker, Assistant Professor > Washington University in St. Louis > Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology > 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 > Phone: (314) 362-2040, Fax: (314) 362-0234 > URL: http://www.biochem.wustl.edu/~baker/ > > > -----Original Message----- > > From: va...@if... > > [mailto:va...@if...] > > Sent: Tuesday, April 06, 2004 6:38 PM > > To: ba...@bi... > > Subject: RE: Very Similar Binding Energies > > > > > > No, I didn't ... I simply tried to see what would give a > > calculation supposing u > > have a set of charges in vacuo vs. what happens with a PB solver. > > > > You mean to reproduce an example of yours: > > > > ddEsolv(upon bind.)= dEsolv(prot+mem) -(dEsolv(prot) + dEsolv(mem)) > > > > where > > > > dEsolv(prot+mem) = E(prot+mem,in water) - E(prot+mem,vacuo) > > dEsolv(prot) = E(prot,in water) - E(prot,vacuo) > > dEsolv(mem) = E(mem,in water) - E(mem,vacuo) > > > > of course with APBS ? > > > > > > Mensaje citado por Nathan Baker <ba...@bi...>: > > > > > Hi Diego -- > > > > > > In addition to the change in Coulombic energy (calculated > > analytically -- > > > did you divide by the protein dielectric in those numbers > > you gave me?) can > > > you also calculate the change in solvation energy upon > > binding? Solvation > > > energy will become more repulsive as the molecules become > > more charged so it > > > may not be too surprising that the overall energy is rather > > close between > > > the two molecules. > > > > > > Thanks, > > > > > > Nathan > > > > > > -- > > > Nathan A. Baker, Assistant Professor > > > Washington University in St. Louis > > > Dept. of Biochemistry and Molecular Biophysics > > > Center for Computational Biology > > > 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 > > > Phone: (314) 362-2040, Fax: (314) 362-0234 > > > URL: http://www.biochem.wustl.edu/~baker/ > > > > > > > -----Original Message----- > > > > From: Diego Vallejo [mailto:va...@if...] > > > > Sent: Monday, April 05, 2004 1:42 PM > > > > To: ba...@bi... > > > > Subject: Very Similar Binding Energies > > > > > > > > > > > > Dear Nathan, > > > > > > > > I have two proteins very very similar to each other. > > > > The 1st is taken from the PDB. The 2nd is a mutation based on > > > > the 1st, made > > > > 'in silico'. > > > > > > > > 1st: Total Charge: -1 > > > > 2nd: Total Charge: +2 > > > > > > > > I want to compute the Binding Energy to a negative membrane > > > > in a certain > > > > position > > > > (Total Q membrane = -128 e, that is -1e per phospholipid) > > > > > > > > So, I thought... things would be very diff'rent... > > > > to my surprise both of the Bind. Enrgies calculations > > give v. similar > > > > results...! > > > > > > > > 1st: Global net energy = -3.051575878752E+02 kJ/mol > > > > 2nd: Global net energy = -3.093793890348E+02 kJ/mol > > > > > > > > I checked, but I have no Idea... > > > > Anything wrong? > > > > > > > > When I did the same calculations close to a neutral membrane, > > > > B.Energies > > > > were +- 1 kj/mol... so everything was 'as if' it was fine... > > > > > > > > I attach the output files... > > > > > > > > thanks > > > > Diego > > > > > > > > > > > > > > > > > > > > > > > > > -----Mensaje original----- > > > > > De: Nathan Baker [mailto:ba...@bi...] > > > > > Enviado el: Lunes, 05 de Abril de 2004 03:19 p.m. > > > > > Para: 'Diego Vallejo' > > > > > CC: Nathan Baker > > > > > Asunto: RE: error in html > > > > > > > > > > > > > > > Fixed -- thanks!! > > > > > > > > > > -- > > > > > Nathan A. Baker, Assistant Professor > > > > > Washington University in St. Louis > > > > > Dept. of Biochemistry and Molecular Biophysics > > > > > Center for Computational Biology > > > > > 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 > > > > > Phone: (314) 362-2040, Fax: (314) 362-0234 > > > > > URL: http://www.biochem.wustl.edu/~baker/ > > > > > > > > > > > -----Original Message----- > > > > > > From: Diego Vallejo [mailto:va...@if...] > > > > > > Sent: Monday, April 05, 2004 12:29 PM > > > > > > To: Nathan Baker > > > > > > Subject: error in html > > > > > > > > > > > > > > > > > > Nathan: > > > > > > > > > > > > in > > > > > > http://agave.wustl.edu/apbs/download/dist/index.html > > > > > > > > > > > > when you click 'Instalation Guide' there is a Not > > found error. > > > > > > It Tries to open: > > > > > > > > http://agave.wustl.edu/apbs/doc/api/html/index.html#installation > > > > > > > > > > > > > > > > > > Saludos > > > > > > > > > > > > Diego Vallejo - die...@md... > > > > > > Licenciado en Física - Universidad Nacional de La Plata. > > > > > > > > > > > > --- > > > > > > Outgoing mail is certified Virus Free. > > > > > > Checked by AVG anti-virus system (http://www.grisoft.com). > > > > > > Version: 6.0.648 / Virus Database: 415 - Release > > Date: 31/03/2004 > > > > > > > > > > > > > > > > > > > > > --- > > > > > Incoming mail is certified Virus Free. > > > > > Checked by AVG anti-virus system (http://www.grisoft.com). > > > > > Version: 6.0.648 / Virus Database: 415 - Release Date: > > 31/03/2004 > > > > > > > > > --- > > > > Outgoing mail is certified Virus Free. > > > > Checked by AVG anti-virus system (http://www.grisoft.com). > > > > Version: 6.0.648 / Virus Database: 415 - Release Date: 31/03/2004 > > > > > > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > This message was sent using IMP, the Internet Messaging Program. > > > > > --- > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.648 / Virus Database: 415 - Release Date: 31/03/2004 > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.760 / Virus Database: 509 - Release Date: 10/09/2004 _______________________________________________ apbs-users mailing list apb...@ch... http://cholla.wustl.edu/mailman/listinfo/apbs-users -- Nathan Baker <ba...@bi...> Dept. of Biochem. & Molec. Biophysics Washington Univ. in St. Louis 700 S. Euclid Ave., Box 8036 St. Louis, MO 63110 Phone: 314-362-2040, Fax: 314-362-0234 URL: http://agave.wustl.edu/ |