[Chimera-users] Forcefields and Molecular Radii

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 25 10:08:52 PDT 2015


Dear Cale,
Bear in mind that the PDB2PQR and APBS tools in Chimera are interfaces to web services running software developed by others (not the Chimera team), so we generally refer to the authors of the software for detailed documentation.

Nevertheless, in the Chimera manual we try to include brief explanations and links to external sites as appropriate. 

(A) I don’t know anything about the TYL06 forcefield specifically, but the Chimera-PDB2PQR manpage gives a literature reference for it that might discuss the radii:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
"TYL06 - a Poisson-Boltzmann-optimized force field (Tang, Yang, and Luo, J Phys Chem B 110:18680 (2006))"
<http://www.ncbi.nlm.nih.gov/pubmed/16970499>

You coulld also text-edit the output PQR file to see the radius values directly.

(2) As described in the Chimera-APBS manpage
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
… smoothed molecular surface is one of the APBS options for mapping dielectric values to 3D coordinates, and there are details at the APBS website: <http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-file-section/elec-keywords/srfm>  

In other words, it is simply one of the ways to partition the grid into low- and high-dielectric areas for the PB calculation.  Choosing a different method will change (perhaps only slightly) the calculated potential values in the output grid.  It doesn’t have anything to do with the shape of surface that Chimera draws later.  It could only affect the values that are mapped onto the Chimera surface with color, and the differences with different partitioning methods may be subtle.

If you actually want to make a smoother surface in Chimera, you could increase vertex density as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#smoothness>
… you may need to reapply the electrostatic coloring after that.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 23, 2015, at 2:15 PM, Cale Martin <cmartin013 at drury.edu> wrote:

> 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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