## RE: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations

 RE: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations From: - 2004-11-26 21:21:39 ```Sorry again, but I'm still getting strange values, so question is: Are salts concentrations important to this calculations?. Thanks Daniel Silva > The most common error in these types of calculations arises when the > "vacuum" calculation has an inhomogeneous dielectric coefficient. What > values of the solvent and solute dielectric coefficients are you using > for the "vacuum" calculations? These should be the same... > > Suppose your protein has a dielectric coefficient of 12 and exists in > different conformations in the apo and holo states. Then you will need > to carry out the following calculations: > > 1) "Solvation energy" of unligated protein in apo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 2) "Solvation energy" of unligated protein in holo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 3) "Solvation energy" of ligated protein in holo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 4) "Solvation energy" of ligand in holo conformation: > a) Calculation with inhomogeneous dielectric (ligand = 12, solvent = > 80) b) Calculation with homogeneous dielectric (ligand = 12, solvent > = 12) > 5) Coulombic energy of unligated protein in apo conformation with > dielectric of 12 > 6) Coulombic energy of unligated protein in holo conformation with > dielectric of 12 > 7) Coulombic energy of ligated protein in holo conformation with > dielectric of 12 > 8) Coulombic energy of ligand in holo conformation with dielectric of > 12 > > You will then have the quantities that can be assembled via a free > energy cycle to give you your binding energy. > > Good luck! > > -- Nathan > > -- > Nathan A. Baker, Assistant Professor > Washington University in St. Louis School of Medicine > 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: apbs-users-admin@... >> [mailto:apbs-users-admin@...] On Behalf Of >> Daniel Adriano Silva Manzano >> Sent: Tuesday, November 23, 2004 3:36 PM >> To: baker@... >> Cc: vkirill@...; apbs-users@...; todd@... >> Subject: [Apbs-users] Sorry I send this mail yesterday but I >> forget Subject: Help about EE calculations >> >> >> >> On Mon, 22 Nov 2004 dsilva@... wrote: >> >> > Nathan Baker, Todd, and APBS users: >> > >> > I'm sorry to make this kind of questions but actually I >> cannot figure >> > how to solve this. >> > >> > As in the tutorial I have a protein that interact with a >> ligand so I >> > made my electrostatic calculations on complex protein and >> ligand with >> > same grid and conditions for every one, then: >> > >> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >> TotalEE_ligand >> > >> > but then I think: if in the tutorial the electrostatic energy of a >> > protein >> > is: >> > electrostatic energy (EE)= TotalEE _vacuum_protein - >> TotalEE _protein >> > >> > then I can make: >> > >> > dGe = EE_complex - EE_protein - EE_ligand >> > >> > but I obtain totally different results as: >> > >> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >> TotalEE_ligand >> > = >> > 6.44 kJ/mol >> > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - >> TotalEE _protein >> > = -287.3 - 6.44 = - 293 >> > >> > So sorry again, but question: >> > why calculus give different results?. >> > >> > >> > This is important to me, because I'm calculating >> electrostatic change >> > of a protein that in the un-liganded state haves a open >> state and in >> > liganded state haves a closed state with ligand inside, >> what made no >> > usefull first method of dGe calculation >> > >> > Thanks >> > >> > Daniel Silva. >> > >> > >> > >> > _______________________________________________ >> > apbs-users mailing list >> > apbs-users@... >> > http://cholla.wustl.edu/mailman/listinfo/apbs-users >> > >> >> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> http://cholla.wustl.edu/mailman/listinfo/apbs-users >> > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users ```

 [Apbs-users] Read potential to set the boundary conditions. From: kirill votyakov - 2004-11-16 18:58:13 ```Dear all, I've faced a problem: I'd like to make a multigrid focusing calculation in APBS and to use the predefined epsilon field. What epsilon field does APBS use on the second step of a multigrid run if we read the epsilon map on the first step. If APBS constructs second epsilon map using the properties of the loaded molecule than a possible solution of this problem can be subsequent manual calculations. Each calculation uses the boundary conditions dirived from the potential calculated on the previous step. Is it possible to read a potential map for seting the boundary conditions? Best Regards, Kirill Votyakov Institute fur Biologiche Information Verarbietung Forshungszentrum Juelich ```
 RE: [Apbs-users] Read potential to set the boundary conditions. From: Nathan Baker - 2004-11-17 14:16:50 ```Hello -- That's an interesting question and I don't really have a good answer. Basically, I think you'd need to do a series of mg-manual calculations and read in separate grids each time. Alternatively, you could read in a very high-resolution dielectric map initially which would generate sufficient detail for subsequent runs. Right now, APBS doesn't make it very easy to convert an mg-auto input file into a series of mg-manual runs. I'll Cc Todd Dolinsky to get his input on how we might do this. Thanks, Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine 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: apbs-users-admin@... > [mailto:apbs-users-admin@...] On Behalf Of > kirill votyakov > Sent: Tuesday, November 16, 2004 10:58 AM > To: apbs-users@... > Subject: [Apbs-users] Read potential to set the boundary conditions. > > > Dear all, > > I've faced a problem: > I'd like to make a multigrid focusing calculation in APBS and > to use the predefined epsilon field. > What epsilon field does APBS use on the second step of a > multigrid run if we read the epsilon map on the first step. > > If APBS constructs second epsilon map using the properties of > the loaded molecule than a possible solution of this problem > can be subsequent manual calculations. Each calculation uses > the boundary conditions dirived from the potential calculated > on the previous step. > > Is it possible to read a potential map for seting the > boundary conditions? > > Best Regards, > Kirill Votyakov > Institute fur Biologiche Information Verarbietung > Forshungszentrum Juelich > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > ```
 RE: [Apbs-users] Read potential to set the boundary conditions. From: - 2004-11-23 04:15:15 ```Nathan Baker, Todd, and APBS users: I'm sorry to make this kind of questions but actually I cannot figure how to solve this. As in the tutorial I have a protein that interact with a ligand so I made my electrostatic calculations on complex protein and ligand with same grid and conditions for every one, then: deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - TotalEE_ligand but then I think: if in the tutorial the electrostatic energy of a protein is: electrostatic energy (EE)= TotalEE _vacuum_protein - TotalEE _protein then I can make: dGe = EE_complex - EE_protein - EE_ligand but I obtain totally different results as: deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - TotalEE_ligand = 6.44 kJ/mol dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - TotalEE _protein = -287.3 - 6.44 = - 293 So sorry again, but question: why calculus give different results?. This is important to me, because I'm calculating electrostatic change of a protein that in the un-liganded state haves a open state and in liganded state haves a closed state with ligand inside, what made no usefull first method of dGe calculation Thanks Daniel Silva. ```
 [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations From: Daniel Adriano Silva Manzano - 2004-11-23 21:36:02 ```On Mon, 22 Nov 2004 dsilva@... wrote: > Nathan Baker, Todd, and APBS users: > > I'm sorry to make this kind of questions but actually I cannot figure how to > solve this. > > As in the tutorial I have a protein that interact with a ligand so I made my > electrostatic calculations on complex protein and ligand with same grid and > conditions for every one, then: > > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - TotalEE_ligand > > but then I think: if in the tutorial the electrostatic energy of a protein > is: > electrostatic energy (EE)= TotalEE _vacuum_protein - TotalEE _protein > > then I can make: > > dGe = EE_complex - EE_protein - EE_ligand > > but I obtain totally different results as: > > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - TotalEE_ligand = > 6.44 kJ/mol > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - TotalEE _protein > = -287.3 - 6.44 = - 293 > > So sorry again, but question: > why calculus give different results?. > > > This is important to me, because I'm calculating electrostatic change of a > protein that in the un-liganded state haves a open state and in liganded > state haves a closed state with ligand inside, what made no usefull first > method of dGe calculation > > Thanks > > Daniel Silva. > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > ```
 RE: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations From: Nathan Baker - 2004-11-24 14:33:11 ```The most common error in these types of calculations arises when the "vacuum" calculation has an inhomogeneous dielectric coefficient. What values of the solvent and solute dielectric coefficients are you using for the "vacuum" calculations? These should be the same... Suppose your protein has a dielectric coefficient of 12 and exists in different conformations in the apo and holo states. Then you will need to carry out the following calculations: 1) "Solvation energy" of unligated protein in apo conformation: a) Calculation with inhomogeneous dielectric (protein = 12, solvent = 80) b) Calculation with homogeneous dielectric (protein = 12, solvent = 12) 2) "Solvation energy" of unligated protein in holo conformation: a) Calculation with inhomogeneous dielectric (protein = 12, solvent = 80) b) Calculation with homogeneous dielectric (protein = 12, solvent = 12) 3) "Solvation energy" of ligated protein in holo conformation: a) Calculation with inhomogeneous dielectric (protein = 12, solvent = 80) b) Calculation with homogeneous dielectric (protein = 12, solvent = 12) 4) "Solvation energy" of ligand in holo conformation: a) Calculation with inhomogeneous dielectric (ligand = 12, solvent = 80) b) Calculation with homogeneous dielectric (ligand = 12, solvent = 12) 5) Coulombic energy of unligated protein in apo conformation with dielectric of 12 6) Coulombic energy of unligated protein in holo conformation with dielectric of 12 7) Coulombic energy of ligated protein in holo conformation with dielectric of 12 8) Coulombic energy of ligand in holo conformation with dielectric of 12 You will then have the quantities that can be assembled via a free energy cycle to give you your binding energy. Good luck! -- Nathan -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine 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: apbs-users-admin@... > [mailto:apbs-users-admin@...] On Behalf Of > Daniel Adriano Silva Manzano > Sent: Tuesday, November 23, 2004 3:36 PM > To: baker@... > Cc: vkirill@...; apbs-users@...; todd@... > Subject: [Apbs-users] Sorry I send this mail yesterday but I > forget Subject: Help about EE calculations > > > > On Mon, 22 Nov 2004 dsilva@... wrote: > > > Nathan Baker, Todd, and APBS users: > > > > I'm sorry to make this kind of questions but actually I > cannot figure > > how to solve this. > > > > As in the tutorial I have a protein that interact with a > ligand so I > > made my electrostatic calculations on complex protein and > ligand with > > same grid and conditions for every one, then: > > > > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - > TotalEE_ligand > > > > but then I think: if in the tutorial the electrostatic energy of a > > protein > > is: > > electrostatic energy (EE)= TotalEE _vacuum_protein - > TotalEE _protein > > > > then I can make: > > > > dGe = EE_complex - EE_protein - EE_ligand > > > > but I obtain totally different results as: > > > > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - > TotalEE_ligand > > = > > 6.44 kJ/mol > > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - > TotalEE _protein > > = -287.3 - 6.44 = - 293 > > > > So sorry again, but question: > > why calculus give different results?. > > > > > > This is important to me, because I'm calculating > electrostatic change > > of a protein that in the un-liganded state haves a open > state and in > > liganded state haves a closed state with ligand inside, > what made no > > usefull first method of dGe calculation > > > > Thanks > > > > Daniel Silva. > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apbs-users@... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > ```
 RE: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations From: - 2004-11-26 21:21:39 ```Sorry again, but I'm still getting strange values, so question is: Are salts concentrations important to this calculations?. Thanks Daniel Silva > The most common error in these types of calculations arises when the > "vacuum" calculation has an inhomogeneous dielectric coefficient. What > values of the solvent and solute dielectric coefficients are you using > for the "vacuum" calculations? These should be the same... > > Suppose your protein has a dielectric coefficient of 12 and exists in > different conformations in the apo and holo states. Then you will need > to carry out the following calculations: > > 1) "Solvation energy" of unligated protein in apo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 2) "Solvation energy" of unligated protein in holo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 3) "Solvation energy" of ligated protein in holo conformation: > a) Calculation with inhomogeneous dielectric (protein = 12, solvent = > 80) b) Calculation with homogeneous dielectric (protein = 12, solvent > = 12) > 4) "Solvation energy" of ligand in holo conformation: > a) Calculation with inhomogeneous dielectric (ligand = 12, solvent = > 80) b) Calculation with homogeneous dielectric (ligand = 12, solvent > = 12) > 5) Coulombic energy of unligated protein in apo conformation with > dielectric of 12 > 6) Coulombic energy of unligated protein in holo conformation with > dielectric of 12 > 7) Coulombic energy of ligated protein in holo conformation with > dielectric of 12 > 8) Coulombic energy of ligand in holo conformation with dielectric of > 12 > > You will then have the quantities that can be assembled via a free > energy cycle to give you your binding energy. > > Good luck! > > -- Nathan > > -- > Nathan A. Baker, Assistant Professor > Washington University in St. Louis School of Medicine > 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: apbs-users-admin@... >> [mailto:apbs-users-admin@...] On Behalf Of >> Daniel Adriano Silva Manzano >> Sent: Tuesday, November 23, 2004 3:36 PM >> To: baker@... >> Cc: vkirill@...; apbs-users@...; todd@... >> Subject: [Apbs-users] Sorry I send this mail yesterday but I >> forget Subject: Help about EE calculations >> >> >> >> On Mon, 22 Nov 2004 dsilva@... wrote: >> >> > Nathan Baker, Todd, and APBS users: >> > >> > I'm sorry to make this kind of questions but actually I >> cannot figure >> > how to solve this. >> > >> > As in the tutorial I have a protein that interact with a >> ligand so I >> > made my electrostatic calculations on complex protein and >> ligand with >> > same grid and conditions for every one, then: >> > >> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >> TotalEE_ligand >> > >> > but then I think: if in the tutorial the electrostatic energy of a >> > protein >> > is: >> > electrostatic energy (EE)= TotalEE _vacuum_protein - >> TotalEE _protein >> > >> > then I can make: >> > >> > dGe = EE_complex - EE_protein - EE_ligand >> > >> > but I obtain totally different results as: >> > >> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >> TotalEE_ligand >> > = >> > 6.44 kJ/mol >> > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - >> TotalEE _protein >> > = -287.3 - 6.44 = - 293 >> > >> > So sorry again, but question: >> > why calculus give different results?. >> > >> > >> > This is important to me, because I'm calculating >> electrostatic change >> > of a protein that in the un-liganded state haves a open >> state and in >> > liganded state haves a closed state with ligand inside, >> what made no >> > usefull first method of dGe calculation >> > >> > Thanks >> > >> > Daniel Silva. >> > >> > >> > >> > _______________________________________________ >> > apbs-users mailing list >> > apbs-users@... >> > http://cholla.wustl.edu/mailman/listinfo/apbs-users >> > >> >> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> http://cholla.wustl.edu/mailman/listinfo/apbs-users >> > > > _______________________________________________ > apbs-users mailing list > apbs-users@... > http://cholla.wustl.edu/mailman/listinfo/apbs-users ```
 Re: [Apbs-users] Sorry I send this mail yesterday but I forget Subject: Help about EE calculations From: Nathan A. Baker - 2004-11-29 13:50:28 ```Yes, definitely. The calculations with homogeneous dielectric should also have zero salt concentration. Thanks, Nathan dsilva@... (11-26-2004 13:20:53-0600): >Sorry again, but I'm still getting strange values, so question is: > >Are salts concentrations important to this calculations?. > >Thanks >Daniel Silva > > >> The most common error in these types of calculations arises when the >> "vacuum" calculation has an inhomogeneous dielectric coefficient. What >> values of the solvent and solute dielectric coefficients are you using >> for the "vacuum" calculations? These should be the same... >> >> Suppose your protein has a dielectric coefficient of 12 and exists in >> different conformations in the apo and holo states. Then you will need >> to carry out the following calculations: >> >> 1) "Solvation energy" of unligated protein in apo conformation: >> a) Calculation with inhomogeneous dielectric (protein = 12, solvent = >> 80) b) Calculation with homogeneous dielectric (protein = 12, solvent >> = 12) >> 2) "Solvation energy" of unligated protein in holo conformation: >> a) Calculation with inhomogeneous dielectric (protein = 12, solvent = >> 80) b) Calculation with homogeneous dielectric (protein = 12, solvent >> = 12) >> 3) "Solvation energy" of ligated protein in holo conformation: >> a) Calculation with inhomogeneous dielectric (protein = 12, solvent = >> 80) b) Calculation with homogeneous dielectric (protein = 12, solvent >> = 12) >> 4) "Solvation energy" of ligand in holo conformation: >> a) Calculation with inhomogeneous dielectric (ligand = 12, solvent = >> 80) b) Calculation with homogeneous dielectric (ligand = 12, solvent >> = 12) >> 5) Coulombic energy of unligated protein in apo conformation with >> dielectric of 12 >> 6) Coulombic energy of unligated protein in holo conformation with >> dielectric of 12 >> 7) Coulombic energy of ligated protein in holo conformation with >> dielectric of 12 >> 8) Coulombic energy of ligand in holo conformation with dielectric of >> 12 >> >> You will then have the quantities that can be assembled via a free >> energy cycle to give you your binding energy. >> >> Good luck! >> >> -- Nathan >> >> -- >> Nathan A. Baker, Assistant Professor >> Washington University in St. Louis School of Medicine >> 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: apbs-users-admin@... >>> [mailto:apbs-users-admin@...] On Behalf Of >>> Daniel Adriano Silva Manzano >>> Sent: Tuesday, November 23, 2004 3:36 PM >>> To: baker@... >>> Cc: vkirill@...; apbs-users@...; todd@... >>> Subject: [Apbs-users] Sorry I send this mail yesterday but I >>> forget Subject: Help about EE calculations >>> >>> >>> >>> On Mon, 22 Nov 2004 dsilva@... wrote: >>> >>> > Nathan Baker, Todd, and APBS users: >>> > >>> > I'm sorry to make this kind of questions but actually I >>> cannot figure >>> > how to solve this. >>> > >>> > As in the tutorial I have a protein that interact with a >>> ligand so I >>> > made my electrostatic calculations on complex protein and >>> ligand with >>> > same grid and conditions for every one, then: >>> > >>> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >>> TotalEE_ligand >>> > >>> > but then I think: if in the tutorial the electrostatic energy of a >>> > protein >>> > is: >>> > electrostatic energy (EE)= TotalEE _vacuum_protein - >>> TotalEE _protein >>> > >>> > then I can make: >>> > >>> > dGe = EE_complex - EE_protein - EE_ligand >>> > >>> > but I obtain totally different results as: >>> > >>> > deltaGelec (dGe)= TotalEE_complex - TotalEE_protein - >>> TotalEE_ligand >>> > = >>> > 6.44 kJ/mol >>> > dGElectrostaticEnergy (EE)= TotalEE _vacuum_protein - >>> TotalEE _protein >>> > = -287.3 - 6.44 = - 293 >>> > >>> > So sorry again, but question: >>> > why calculus give different results?. >>> > >>> > >>> > This is important to me, because I'm calculating >>> electrostatic change >>> > of a protein that in the un-liganded state haves a open >>> state and in >>> > liganded state haves a closed state with ligand inside, >>> what made no >>> > usefull first method of dGe calculation >>> > >>> > Thanks >>> > >>> > Daniel Silva. >>> > >>> > >>> > >>> > _______________________________________________ >>> > apbs-users mailing list >>> > apbs-users@... >>> > http://cholla.wustl.edu/mailman/listinfo/apbs-users >>> > >>> >>> _______________________________________________ >>> apbs-users mailing list >>> apbs-users@... >>> http://cholla.wustl.edu/mailman/listinfo/apbs-users >>> >> >> >> _______________________________________________ >> apbs-users mailing list >> apbs-users@... >> http://cholla.wustl.edu/mailman/listinfo/apbs-users > > End of message from dsilva@... -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine 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 PGP key: http://cholla.wustl.edu/~baker/pubkey.asc ```