Thread: [Apbs-users] per-residue decomposition
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From: Dimitrios S. <dim...@gm...> - 2010-05-20 14:32:05
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Dear APBS Users, has anybody implemented a method to decompose on a per-residue basis the values of solvation energy? 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 |
From: Nathan B. <nat...@gm...> - 2010-05-20 23:56:57
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Hi Dimitrios -- Are you referring to the strictly-electrostatic contribution (i.e., no changes to the dielectric barrier; only changes to charge distribution) or the entire (dielectric and charge) contribution to the polar solvation energy? Thanks, Nathan On 5/20/2010 9:31 AM, Dimitrios Spiliotopoulos wrote: > > Dear APBS Users, > > has anybody implemented a method to decompose on a per-residue basis the > values of solvation energy? > > 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... > <mailto:spi...@hs...>; dim...@gm... > <mailto:dim...@gm...> > Skype: dimitris3.16 > > > > ------------------------------------------------------------------------------ > > > > > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users |
From: Dimitrios S. <dim...@gm...> - 2010-05-21 07:37:10
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Dear prof. Baker, I was thinking of the entire contribution to the polar solvation energy. 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 2010/5/21 Nathan Baker <nat...@gm...> > Hi Dimitrios -- > > Are you referring to the strictly-electrostatic contribution (i.e., no > changes to the dielectric barrier; only changes to charge distribution) or > the entire (dielectric and charge) contribution to the polar solvation > energy? > > Thanks, > > Nathan > > > On 5/20/2010 9:31 AM, Dimitrios Spiliotopoulos wrote: > >> >> Dear APBS Users, >> >> has anybody implemented a method to decompose on a per-residue basis the >> values of solvation energy? >> >> Thank you very much in advance! >> >> Dimitrios Spiliotopoulos >> >> > >> >> >> >> ------------------------------------------------------------------------------ >> >> >> >> >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> > |
From: Nathan B. <nat...@gm...> - 2010-05-21 20:21:40
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Hi Dimitrios -- In that case, there is no shortcut: you need to run each calculation independently. -- Nathan On 5/21/2010 2:37 AM, Dimitrios Spiliotopoulos wrote: > > Dear prof. Baker, > > I was thinking of the entire contribution to the polar solvation energy. > > 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... > <mailto:spi...@hs...>; dim...@gm... > <mailto:dim...@gm...> > Skype: dimitris3.16 > > > > > > > > > 2010/5/21 Nathan Baker <nat...@gm... > <mailto:nat...@gm...>> > > Hi Dimitrios -- > > Are you referring to the strictly-electrostatic contribution (i.e., > no changes to the dielectric barrier; only changes to charge > distribution) or the entire (dielectric and charge) contribution to > the polar solvation energy? > > Thanks, > > Nathan > > > On 5/20/2010 9:31 AM, Dimitrios Spiliotopoulos wrote: > > > Dear APBS Users, > > has anybody implemented a method to decompose on a per-residue > basis the > values of solvation energy? > > Thank you very much in advance! > > Dimitrios Spiliotopoulos > > > > > > ------------------------------------------------------------------------------ > > > > > _______________________________________________ > apbs-users mailing list > apb...@li... > <mailto:apb...@li...> > https://lists.sourceforge.net/lists/listinfo/apbs-users > > |
From: Dimitrios S. <dim...@gm...> - 2010-05-24 11:54:26
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Dear prof Baker, thank you very much for your answer. Before proceeding in my calculations, I'd like to make sure I understood correctly. By "each calculation" you mean a thermodynamic cycle comprehending complex, AAofinterest complex_withoutAAofinterest (i.e., calculating the free energies for the PQR files of the complex, the residue and the complex upon removal of the residue of interest)? If so, that would be similar to what is explained for the pKa calculations in the seventh chapter of the tutorial at http://nehru.mat.upm.es/cgi-bin/dwww/usr/share/doc/apbs/html/tutorial/ but without zeroing out the charges for any atom. Am I correct? 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 2010/5/21 Nathan Baker <nat...@gm...> > Hi Dimitrios -- > > In that case, there is no shortcut: you need to run each calculation > independently. > > -- Nathan > > > On 5/21/2010 2:37 AM, Dimitrios Spiliotopoulos wrote: > >> >> Dear prof. Baker, >> >> I was thinking of the entire contribution to the polar solvation energy. >> >> 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... >> <mailto:spi...@hs...>; dim...@gm... >> <mailto:dim...@gm...> >> >> Skype: dimitris3.16 >> >> >> >> >> >> >> >> >> 2010/5/21 Nathan Baker <nat...@gm... >> <mailto:nat...@gm...>> >> >> >> Hi Dimitrios -- >> >> Are you referring to the strictly-electrostatic contribution (i.e., >> no changes to the dielectric barrier; only changes to charge >> distribution) or the entire (dielectric and charge) contribution to >> the polar solvation energy? >> >> Thanks, >> >> Nathan >> >> >> On 5/20/2010 9:31 AM, Dimitrios Spiliotopoulos wrote: >> >> >> Dear APBS Users, >> >> has anybody implemented a method to decompose on a per-residue >> basis the >> values of solvation energy? >> >> Thank you very much in advance! >> >> Dimitrios Spiliotopoulos >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> >> >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> <mailto:apb...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> >> >> |
From: Nathan B. <nat...@gm...> - 2010-05-25 01:25:16
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Hi Dimitrios - You can get the per-residue contribution to any free energy by performing two calculations, one with the residue of interest and one without the residue, and then taking the difference of energies between the two calculations. In other words, this process is similar to the intrinsic pKa example you mentioned but could be generalized to other processes as well. Nathan From: Dimitrios Spiliotopoulos [mailto:dim...@gm...] Sent: Monday, May 24, 2010 6:54 AM To: Nathan Baker Cc: APBS Users Mailing List Subject: Re: [Apbs-users] per-residue decomposition Dear prof Baker, thank you very much for your answer. Before proceeding in my calculations, I'd like to make sure I understood correctly. By "each calculation" you mean a thermodynamic cycle comprehending complex, AAofinterest complex_withoutAAofinterest (i.e., calculating the free energies for the PQR files of the complex, the residue and the complex upon removal of the residue of interest)? If so, that would be similar to what is explained for the pKa calculations in the seventh chapter of the tutorial at http://nehru.mat.upm.es/cgi-bin/dwww/usr/share/doc/apbs/html/tutorial/ but without zeroing out the charges for any atom. Am I correct? 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 2010/5/21 Nathan Baker <nat...@gm...> Hi Dimitrios -- In that case, there is no shortcut: you need to run each calculation independently. -- Nathan On 5/21/2010 2:37 AM, Dimitrios Spiliotopoulos wrote: Dear prof. Baker, I was thinking of the entire contribution to the polar solvation energy. 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... <mailto:spi...@hs...>; dim...@gm... <mailto:dim...@gm...> Skype: dimitris3.16 2010/5/21 Nathan Baker <nat...@gm... <mailto:nat...@gm...>> Hi Dimitrios -- Are you referring to the strictly-electrostatic contribution (i.e., no changes to the dielectric barrier; only changes to charge distribution) or the entire (dielectric and charge) contribution to the polar solvation energy? Thanks, Nathan On 5/20/2010 9:31 AM, Dimitrios Spiliotopoulos wrote: Dear APBS Users, has anybody implemented a method to decompose on a per-residue basis the values of solvation energy? Thank you very much in advance! Dimitrios Spiliotopoulos ---------------------------------------------------------------------------- -- _______________________________________________ apbs-users mailing list apb...@li... <mailto:apb...@li...> https://lists.sourceforge.net/lists/listinfo/apbs-users |