VMD-L Mailing List

From: Sebastian Maximilian Wilhelm (Sebastian.Wilhelm_at_rwth-aachen.de)
Date: Thu Apr 14 2011 - 10:31:34 CDT

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