VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 14:51:08 CST

Hi,
  There's no need to re-post. If you're not getting any answers, it's
either because the question is unclearly stated, or others don't know the
answer. My own guess is that the behavior for response of SASA and SESA
may depend on the specific values of probe radius that you're using. You
didn't say what probe radii you are actually trying, so it's hard to give
a general answer. For a probe radius near infinity, you'll get the area of
a convex hull surrounding the structure. For a probe radius of zero, you'll
get the surface area corresponding to the "union of balls". Presumably you
are trying values that are close to the 1.4 A radius of a water molecule,
but you haven't indicated to what degree you have increased the probe radius
nor what your solute structure looks like. I think you may come up with your
own explanation if you look very carefully at the MSMS surface that's
generated for the probe radii you have selected. Failing this, you may
want to discuss it with Michel Sanner, the primary author of MSMS, as it
might be an unusual behavior of MSMS itself under your particular test
circumstance. Do you get the same result with other SASA calculation tools?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jan 24, 2010 at 01:44:45PM -0700, Khaled Barakat wrote:
> Hello,
>
> I am trying to calculate the solvent accessible/excluded surface area (SASA and SESA) using MSMS for different probe
> radii. I noticed that the SASA increases with increasing the probe radius, while the SESA decreases. My question is:
> Does these results make sense?! I was expecting opposite results ( i.e. the SASA decreases with increasing the probe
> radius, because a larger solvent molecule will not be able to touch the surface of the protein as much as a smaller solvent
> molecule).
>
> I will appreciate if someone can help me understand these results.
>
> Thanks in advance.
> Khaled
>
> My numbers are:
>
> Radius SASA SESA
> 2.5 7869.7254 5957.5241
> 2.8 7936.7443 5832.3499
> 3.0 7990.4262 5782.2308
> 4.25 8535.3977 5491.1256
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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