Re: [apbs-users] output potential at specific point in space
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Re: [apbs-users] output potential at specific point in space
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From: Baker, N. <Nat...@pn...> - 2012-03-14 06:21:51
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Hello -- Please look at the multivalue tool which has been discussed on this mailing list in the past. This tool will provide the value of the potential at user-specified locations in the solution domain. Good luck, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me -----Original Message----- From: Rosana Collepardo [mailto:r.c...@gm...] Sent: Monday, March 12, 2012 7:21 AM To: apb...@li... Subject: [apbs-users] output potential at specific point in space Hello, I would like to know if it is possible to set up an apbs calculation to output the potential of a macromolecule at an specific point in space. I'm trying to do something like in Rohs et al., The role of DNA shape in protein-DNA recognition, Nature 461, 1248-1253 (2009) http://www.nature.com/nature/journal/v461/n7268/full/nature08473.html : "Electrostatic potentials were obtained from solutions to the non-linear Poisson-Boltzman equation at physiological ionic strength using the DelPhi program. Regions inside the molecular surface of the DNA were assigned a dielectric constant of 2, whereas the solvent was assigned a value of 80. The potential is reported at a reference point at the centre of the minor groove. The reference point is located close to the bottom of the groove in approximately the plane of a base pair. This definition provides a measure of electrostatic potential as a function of base sequence. " Many thanks, Rosana ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ apbs-users mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-users |