[Chimera-users] Interpreting field / force direction in Coulombic Surface Coloring
harjanto.sumitro at gmail.com
Sun May 20 04:39:24 PDT 2012
Hi elaine, so does blue patch (positive interaction energy) mean positively
charged or negatively charged surface?
On May 19, 2012 1:16 AM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> Hi Sumitro,
> The interaction energy of a "test" charge at some point would be the
> charge multiplied by the electrostatic potential. So if the test charge
> is -1 e (like one electron) its interaction energy at a point with
> potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive
> potential favors interaction with negative charges and vice versa.
> I hope this clarifies,
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> P.S. better to send questions to chimera-users at cgl.ucsf.edu because if
> you send to me and I'm on vacation, you might not get answered
> On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote:
> > Hi Elaine,
> > I have a simple question regarding the Coulombic Surface Coloring. I
> understand that the potential are generated by assuming a charged probe
> that moves along the surface of the model and as it traverses the surface
> the potential is picked up as the calculated electrostatic force the probe
> should experience (that's my understanding, correct me if I'm wrong please).
> > I am just, however, a little confused about the interpretation of the
> value. say if I got a blue patch on the surface, which means I'm getting
> values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean
> the region indicated by the blue patch should potential attract or repel
> > Thanks!
> > Cheers,
> > Sumitro
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