Thread: [Apbs-users] per atom potential problem
Biomolecular electrostatics software
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From: david z. <pp...@ya...> - 2007-02-14 18:42:21
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hi, I am using apbs_tools.py to genrate potential dx file and also output per atom potential. When I visualize molecular surface colored by potential on sovent accessible surface in pymol, I fount it is not consistent with per atom potential. Using pdb1a0a as an example, B chain THR resid 62 shows red (which means negative potential) in pymol, but all of its atoms potentials are greater than 0. My another question is: may I output per atom potential with unit KT/e, not KJ/mol? thanks, david --------------------------------- Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. |
From: Nathan B. <ba...@cc...> - 2007-02-15 15:52:22
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Hi David -- > hi, I am using apbs_tools.py to genrate potential dx file and also > output per atom potential. When I visualize molecular surface > colored by potential on sovent accessible surface in pymol, I fount > it is not consistent with per atom potential. It's not obvious to me why you would expect the potential on the surface to be equal to the potential at the charge centers, as reported by APBS. The spatial different between these potential values can result in significant differences in potential values. Agreement between these values is particularly unlikely for the potential on the solvent-accessible surface which is even further from the charge centers -- one might expect slightly better agreement for surface potentials plotted on the van der Waals or molecule surface... > Using pdb1a0a as an example, B chain THR resid 62 shows red (which > means negative potential) in pymol, but all of its atoms potentials > are greater than 0. This is likely due to nonlocal effects -- try decreasing the surface distance to van der Waals or molecular surface distances and see if the answer changes. It often does; this is partly the reason why I prefer solvent-accessible surfaces for potential visualization: they give a much more "global" view of the surface properties. > My another question is: may I output per atom potential with unit > KT/e, not KJ/mol? Are you referring to the output from the apbs_tools.py script or the OpenDX file? Thanks, Nathan > thanks, > > david > > Never miss an email again! > Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV________________________________ > _______________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |