VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 15 2011 - 16:03:05 CDT

Sebastian,
  I don't expect the "density" of SASA samples to vary across the surface
of the molecule much, but I would indeed expect some atoms to be only
partially covered by sample points, or to have no sample points on their
surface. Could you send me an example structure file that reproduces
your problem, along with a text file containing the point set that
VMD produced when run on your machine? If the files are large, please
gzip them and/or post them on the web so I can download them rather than
sending via email.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 14, 2011 at 05:31:34PM +0200, Sebastian Maximilian Wilhelm wrote:
> Hi,
>
> i have written a little script which calculates the SASA with srad = 0.0 (for determination of the surface area of one molecule) for a molecule with three sites (index 0 1 2) and prints out every vector which is written to 'Punkte':
>
> set mol [atomselect top "index 0 1 2"]
> set nichtmol [atomselect top "not index 0 1 2"]
>
> set a [measure sasa 0.0 $mol -points Punkte -restrict $nichtmol]
>
> set l [llength $Punkte]
> graphics 0 color red
>
> for {set i 0} {$i < $l} {incr i} {
>
> set b [lindex $Punkte $i]
> graphics 0 point $b
>
> }
>
> When I look at the resulting plot, I see the original molecule (index 0 1 2) and all points directly on its surface (because of srad = 0.0). On the surface there are regions with high concentrations of points and some other regions of the surface with no points. To my point of view it means, that these regions with lower a concentration of points are not accessible by the solvent. I analyzed propane and to my surprise, the regions where the atoms in one propane molecule penetrate each other have higher concentrations of points than the regions which are thougt to be the contact places to other propane molecules.
>
> My questions are now: how does VMD calculate these regions? Is there any nearer specification for the solvent (size or shape)? Are the regions with a lower concentration of points blocked by other molecules?
>
>
> Thanks in advance!
> Sebastian Wilhelm 

-- 
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