## Re: [Apbs-users] Problem with neutral Arg

 Re: [Apbs-users] Problem with neutral Arg From: L. Michel Espinoza-Fonseca - 2009-08-20 15:06:12 Attachments: Message as HTML ```Hi What previous post are you talking about? Before we can help you please help us by pointing out your original post. > regarding my previous post: > So to calculate a binding energy, following the recent review that i've > read in meth. cell. biology, to calculate the polar contribution to the > binding energy one would follow this formula: > > ΔG(complex-reference) - ΔG(complex-water) - ΔG(mol2-water) - ΔG(mol2-reference) > - ΔG(mol1-water) - ΔG(mol1-reference) = ΔGsolvation > > ΔGcouloumb= ΔGcouloumb(complex) - ( ΔGcouloumb(mol1) + ΔGcouloumb(mol2) ) > > polar contribution to the binding energy = ΔGsolvation+ΔGcouloumb > This is partly correct. The polar contribution to the free energy of binding is deltaG(polar)= deltadeltaG(solvation) + deltadeltaG(coulomb) > > The reference is represented by putting the dielectric value in solvent and > solute equal ( like for example 2)? > The reference should be the dielectric constant of vacuum (epsilon=1). > > So retrieving the input files (as starting point) from the pdb2pqr and > doing the math we have the value, is this right? > The apolar part isn't contemplated in APBS? Any alternative on doing this > apolar contribution to binding calculation? > The apolar solvation energy can be approximated by calculated by using the solvent-accessible surface area (As described in the original MM/PBSA method; see Kollman et al., Acc. Chem. Res. 2000, 33, 889). Alternatively, the apolar solvation energy can be estimated using APBS ( http://bakergroup.wustl.edu/baker/classes/BME-540/2008/apbs-tutorial/#id450929). The apolar contribution to the free energy of binding will be simply the sum of the van der Waals energy plus the apolar solvation energy. Best, Michel > thanks > > tiago > > > > ------------------------------------------------------------------------------ > 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 > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > ```

 [Apbs-users] Problem with neutral Arg From: kiranmayee bakshy - 2009-08-19 07:32:04 Attachments: Message as HTML ```Hi, I wanted to calculate the electrostatic potential of a protein at pH 9.5 where one of the Arg residue displays a neutral charge. The force fields (all) being used by PDB2PQR do not support this. Can anybody please help me with this. It gives the output with a default pH 7 even when the pH is set to 9.5 Thanks Kiranmayee ```
 Re: [Apbs-users] Problem with neutral Arg From: Yong Huang - 2009-08-19 15:03:57 Attachments: Message as HTML ```Hello, Sorry for the inconvenience, this is something that the current PDB2PQR version cannot deal with. We will start a new tracker item for this issue, and hopefully address this issue before the next release. Thanks, Yong On Wed, Aug 19, 2009 at 2:31 AM, kiranmayee bakshy < kiranmayee_bakshy@...> wrote: > Hi, > I wanted to calculate the electrostatic potential of a protein at pH 9.5 > where one of the Arg residue displays a neutral charge. The force fields > (all) being used by PDB2PQR do not support this. Can anybody please help me > with this. It gives the output with a default pH 7 even when the pH is set > to 9.5 > > Thanks > Kiranmayee > > > > ------------------------------------------------------------------------------ > 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 > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Yong Huang, D.Sc. Center for Computational Biology Washington University School of Medicine ```
 Re: [Apbs-users] Problem with neutral Arg From: Gernot Kieseritzky - 2009-08-19 16:10:03 ```Hi! The easiest way to overcome this problem is to simply symmetrically remove a net charge of +1 from the guanidine group of Arg. For example you just subtract 1/9 from the partial charges of HE, NE, CZ, NH1, HH*, NH2 and HH*. That is good first approximation. Better however is calculate CHELP-like partial charges obtained from the electrostatic potential of neutral Arg in vacuum computed from the wave function. Jaguar and Gauss can do this for you -- and it's comparably cheap. You could also try to submit your protein to our Karlsberg+ web service if it's not too large: http://agknapp.chemie.fu-berlin.de/karlsberg/ (I would do a single conformation computation in this case). It's primary focus is calculating the pKA of a titratable residue like Arginine. After the computation it allows you to download a PQR file including charges set to the most probable state (such as your neutralized Arginine). It would be interesting to see what's the pKA of your arginine. Internally, Karlsberg+ uses APBS to evaluate electrostatic energies. Greetings, Gernot Kieseritzky On Wed, 2009-08-19 at 00:31 -0700, kiranmayee bakshy wrote: > Hi, > I wanted to calculate the electrostatic potential of a protein at pH > 9.5 where one of the Arg residue displays a neutral charge. The force > fields (all) being used by PDB2PQR do not support this. Can anybody > please help me with this. It gives the output with a default pH 7 even > when the pH is set to 9.5 > > Thanks > Kiranmayee > > > ------------------------------------------------------------------------------ > 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 apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [Apbs-users] Problem with neutral Arg From: Nathan Baker - 2009-08-19 19:20:01 ```Thanks, Gernot! On Aug 19, 2009, at 11:09 AM, Gernot Kieseritzky wrote: > Hi! > The easiest way to overcome this problem is to simply symmetrically > remove a net charge of +1 from the guanidine group of Arg. For example > you just subtract 1/9 from the partial charges of HE, NE, CZ, NH1, > HH*, > NH2 and HH*. That is good first approximation. Better however is > calculate CHELP-like partial charges obtained from the electrostatic > potential of neutral Arg in vacuum computed from the wave function. > Jaguar and Gauss can do this for you -- and it's comparably cheap. > > You could also try to submit your protein to our Karlsberg+ web > service > if it's not too large: > > http://agknapp.chemie.fu-berlin.de/karlsberg/ > > (I would do a single conformation computation in this case). > > It's primary focus is calculating the pKA of a titratable residue like > Arginine. After the computation it allows you to download a PQR file > including charges set to the most probable state (such as your > neutralized Arginine). It would be interesting to see what's the pKA > of > your arginine. Internally, Karlsberg+ uses APBS to evaluate > electrostatic energies. > > Greetings, > Gernot Kieseritzky > > On Wed, 2009-08-19 at 00:31 -0700, kiranmayee bakshy wrote: >> Hi, >> I wanted to calculate the electrostatic potential of a protein at pH >> 9.5 where one of the Arg residue displays a neutral charge. The force >> fields (all) being used by PDB2PQR do not support this. Can anybody >> please help me with this. It gives the output with a default pH 7 >> even >> when the pH is set to 9.5 >> >> Thanks >> Kiranmayee >> >> >> ------------------------------------------------------------------------------ >> 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 apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users > > > ------------------------------------------------------------------------------ > 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 > apbs-users@... > 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/ ```
 Re: [Apbs-users] Problem with neutral Arg From: Tiago Lopes Gomes - 2009-08-20 14:33:44 Attachments: Message as HTML ```hello, regarding my previous post: So to calculate a binding energy, following the recent review that i've read in meth. cell. biology, to calculate the polar contribution to the binding energy one would follow this formula: ΔG(complex-reference) - ΔG(complex-water) - ΔG(mol2-water) - ΔG(mol2-reference) - ΔG(mol1-water) - ΔG(mol1-reference) = ΔGsolvation ΔGcouloumb= ΔGcouloumb(complex) - ( ΔGcouloumb(mol1) + ΔGcouloumb(mol2) ) polar contribution to the binding energy = ΔGsolvation+ΔGcouloumb The reference is represented by putting the dielectric value in solvent and solute equal ( like for example 2)? So retrieving the input files (as starting point) from the pdb2pqr and doing the math we have the value, is this right? The apolar part isn't contemplated in APBS? Any alternative on doing this apolar contribution to binding calculation? thanks tiago ```
 Re: [Apbs-users] Problem with neutral Arg From: L. Michel Espinoza-Fonseca - 2009-08-20 15:06:12 Attachments: Message as HTML ```Hi What previous post are you talking about? Before we can help you please help us by pointing out your original post. > regarding my previous post: > So to calculate a binding energy, following the recent review that i've > read in meth. cell. biology, to calculate the polar contribution to the > binding energy one would follow this formula: > > ΔG(complex-reference) - ΔG(complex-water) - ΔG(mol2-water) - ΔG(mol2-reference) > - ΔG(mol1-water) - ΔG(mol1-reference) = ΔGsolvation > > ΔGcouloumb= ΔGcouloumb(complex) - ( ΔGcouloumb(mol1) + ΔGcouloumb(mol2) ) > > polar contribution to the binding energy = ΔGsolvation+ΔGcouloumb > This is partly correct. The polar contribution to the free energy of binding is deltaG(polar)= deltadeltaG(solvation) + deltadeltaG(coulomb) > > The reference is represented by putting the dielectric value in solvent and > solute equal ( like for example 2)? > The reference should be the dielectric constant of vacuum (epsilon=1). > > So retrieving the input files (as starting point) from the pdb2pqr and > doing the math we have the value, is this right? > The apolar part isn't contemplated in APBS? Any alternative on doing this > apolar contribution to binding calculation? > The apolar solvation energy can be approximated by calculated by using the solvent-accessible surface area (As described in the original MM/PBSA method; see Kollman et al., Acc. Chem. Res. 2000, 33, 889). Alternatively, the apolar solvation energy can be estimated using APBS ( http://bakergroup.wustl.edu/baker/classes/BME-540/2008/apbs-tutorial/#id450929). The apolar contribution to the free energy of binding will be simply the sum of the van der Waals energy plus the apolar solvation energy. Best, Michel > thanks > > tiago > > > > ------------------------------------------------------------------------------ > 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 > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > ```
 Re: [Apbs-users] Problem with neutral Arg From: Tiago Lopes Gomes - 2009-08-20 16:51:55 Attachments: Message as HTML ```Hi The previous was related to the input file setup, not directly to do with this one. Just to know how to set grid dimensions and another parameters, before i started the calculations. So it means that to calculate the energy of the reference compound i would have to put pdie=1 and sdie=1, or pdie=2 and sdie=1? going to check the articles and the user guide for the apolar parts thanks a lot tiago I post the previous post here with the answers : Hello -- i am studying the interaction between a peptide (13 aa) and a protein > ( 44 aa), and i would like to compute the binding energy following the > thermodynamic cycle included in the tutorials. A few questions, > > How one knows the parameters t use for the calculations namely the > grid dimensions ( grid and dime parameters). > I would use a program like PDB2PQR (http://pdb2pqr.sf.net/) as a starting point. For quantitative calculations, I would recommend a grid spacing of less than 0.5 Å; for qualitative, a grid spacing of ~0.5 Å should be OK. Regardless, you should test your results to be sure that your conclusions are not sensitive to the choice of grid spacing. Which apbs.in shall i use from the examples directory. Does one need to use > the psize.py to do > this automatic, like in the GUI. If yes how? > PDB2PQR will generate an APBS input file for you to use as a starting point. Does the program does this automatic if i choose mg-auto? > No, I would recommend reading the documentation at http://apbs.wustl.edu/ and pay particular attention to the ELEC section ( http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section). Good luck, Nathan I tried also different force fields in generating pqr files (Amber and > Parse), with different results, i guess is is normal, i don't know > what is the most appropriate forcefield ( maybe depends on the system > studied) > > If i missed any tutorial pleased point me to it. > > thanks, > > bye > tiago ```
 Re: [Apbs-users] Problem with neutral Arg From: Nathan Baker - 2009-08-21 01:27:00 Attachments: Message as HTML ```Hello -- You can construct a free energy cycle to make either contribution work. However, if you want to use the analytic version of Coulomb's law, then you need to use a reference state with pdie = sdie. -- Nathan On Aug 20, 2009, at 11:51 AM, Tiago Lopes Gomes wrote: > Hi > > The previous was related to the input file setup, not directly to do > with this one. Just to know how to set grid dimensions and another > parameters, before i started the calculations. > So it means that to calculate the energy of the reference compound i > would have to put pdie=1 and sdie=1, or pdie=2 and sdie=1? > going to check the articles and the user guide for the apolar parts > > thanks a lot > > tiago > > > I post the previous post here with the answers : > > Hello -- > > > i am studying the interaction between a peptide (13 aa) and a protein > ( 44 aa), and i would like to compute the binding energy following the > thermodynamic cycle included in the tutorials. A few questions, > > How one knows the parameters t use for the calculations namely the > grid dimensions ( grid and dime parameters). > > I would use a program like PDB2PQR (http://pdb2pqr.sf.net/) as a > starting point. For quantitative calculations, I would recommend a > grid spacing of less than 0.5 Å; for qualitative, a grid spacing of > ~0.5 Å should be OK. Regardless, you should test your results to be > sure that your conclusions are not sensitive to the choice of grid > spacing. > > > Which apbs.in shall i use from the examples directory. Does one need > to use the psize.py to do > this automatic, like in the GUI. If yes how? > > PDB2PQR will generate an APBS input file for you to use as a > starting point. > > > Does the program does this automatic if i choose mg-auto? > > No, I would recommend reading the documentation at http://apbs.wustl.edu/ > and pay particular attention to the ELEC section (http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section > ). > > Good luck, > > Nathan > > I tried also different force fields in generating pqr files (Amber and > Parse), with different results, i guess is is normal, i don't know > what is the most appropriate forcefield ( maybe depends on the system > studied) > > If i missed any tutorial pleased point me to it. > > thanks, > > bye > tiago > ------------------------------------------------------------------------------ > 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 > apbs-users@... > 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/ ```