[Chimera-users] Forcefields and Molecular Radii

Cale Martin cmartin013 at drury.edu
Wed Sep 23 14:15:24 PDT 2015


Dear Chimera users,

Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein.  I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER.  When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term.  Is this a function of the forcefield in any way?  Should this be expected from these two different forcefields?

Another issue that I have had along the same line involves the APBS program.  The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same.  Should this setting affect the visualization of my molecule surface in any way?

Thank you,
Cale Martin
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