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Re: [Apbs-users] APBS examples
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From: Joachim R. <Rei...@gb...> - 2003-04-01 17:21:17
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Nathan A. Baker schrieb am 04/01/2003 05:03 PM: >Dear Joachim -- > >Please see apbs/tools/manip/coulomb; that will give you the _vacuum_ >electrostatic/coulombic energy (i.e., will need to be scaled by the >appropriate dielectric constant). > Thanks for the prompt anwer! So I did 3 calculations an got: FKBP/1d7i-dss> ~/apbs-0.2.6/tools/manip/coulomb complex.pqr Setting up atom list from complex.pqr Read 1677 atoms Using vacuum dielectric, distance in Ang, and charge in e.... Calculating... ------------------------------------------------------- Total energy = -1.330929222200e+05 kJ/mol in vacuum. Total x-force = 1.497303440158e-13 kJ/mol/A in vacuum. Total y-force = -6.585724990311e-13 kJ/mol/A in vacuum. Total z-force = -1.748561200538e-12 kJ/mol/A in vacuum. FKBP/1d7i-dss> ~/apbs-0.2.6/tools/manip/coulomb 1d7i-min.pqr Setting up atom list from 1d7i-min.pqr Read 1663 atoms Using vacuum dielectric, distance in Ang, and charge in e.... Calculating... ------------------------------------------------------- Total energy = -1.326437989481e+05 kJ/mol in vacuum. Total x-force = -2.313740527245e-13 kJ/mol/A in vacuum. Total y-force = -2.843972731406e-13 kJ/mol/A in vacuum. Total z-force = -1.099026750442e-12 kJ/mol/A in vacuum. FKBP/1d7i-dss> ~/apbs-0.2.6/tools/manip/coulomb dss-min.pqr Setting up atom list from dss-min.pqr Read 14 atoms Using vacuum dielectric, distance in Ang, and charge in e.... Calculating... ------------------------------------------------------- Total energy = -4.251892874134e+02 kJ/mol in vacuum. Total x-force = -6.025365956368e-16 kJ/mol/A in vacuum. Total y-force = -8.435512338916e-15 kJ/mol/A in vacuum. Total z-force = 1.446087829528e-14 kJ/mol/A in vacuum. FKBP/1d7i-dss> Building differences I get -23.933984486600 kJ/mol/A in vacuum. but -11.9670 is stated in the docs. So my question is now: How to scale? Or what is wrong here? > >Thanks, > >Nathan > >Joachim Reichelt <Rei...@gb...> (04-01-2003 16:59:44+0200): > > >>Dear all, >> >>I want to recalculate one of the examles: FKBP >>I wonder where to get DGbind(Coul.) >> >>Can you give me a hint? >>I want to get the reaction energie of a compex. >> >> >>-- >>Mit freundlichen Gruessen Best Regards >> >> Joachim Reichelt >> >> SB - Strukturbiologie >> GBF - Gesellschaft fuer Biotechnologische Forschung >> German Research Centre for Biotechnology >> >>WWW: http://www.gbf.de _/_/_/ _/_/_/ _/_/_/_/ >>EMAIL: REI...@gb... _/ _/ _/ _/ _/ >> _/ _/ _/ _/ >>Mascheroder Weg 1 _/ _/ _/_/_/ _/_/_/ >>D-38124 Braunschweig _/ _/ _/ _/ _/ >>Tel: +(49) 531 6181 352 _/ _/ _/ _/ _/ >>FAX: +(49) 531 2612 388 _/_/_/ _/_/_/ _/ >> >>http://struktur.gbf.de/ >> >>-- Disclaimer -- >>Standard > Keyword : Opinions, my own, nobody else's, whatsoever ... >> >>Man muss sich notfalls jemand mieten, >>hat man an Geist selbst nichts zu bieten! (Heinz Erhardt) >> >>_______________________________________________ >>apbs-users mailing list >>apb...@ch... >>http://cholla.wustl.edu/mailman/listinfo/apbs-users >> >> >End of message from Joachim Reichelt. > > > -- Mit freundlichen Gruessen Best Regards Joachim Reichelt SB - Strukturbiologie GBF - Gesellschaft fuer Biotechnologische Forschung German Research Centre for Biotechnology WWW: http://www.gbf.de _/_/_/ _/_/_/ _/_/_/_/ EMAIL: REI...@gb... _/ _/ _/ _/ _/ _/ _/ _/ _/ Mascheroder Weg 1 _/ _/ _/_/_/ _/_/_/ D-38124 Braunschweig _/ _/ _/ _/ _/ Tel: +(49) 531 6181 352 _/ _/ _/ _/ _/ FAX: +(49) 531 2612 388 _/_/_/ _/_/_/ _/ http://struktur.gbf.de/ -- Disclaimer -- Standard > Keyword : Opinions, my own, nobody else's, whatsoever ... Man muss sich notfalls jemand mieten, hat man an Geist selbst nichts zu bieten! (Heinz Erhardt) |