VMD-L Mailing List

From: Matthew Wilce (Matthew.Wilce_at_med.monash.edu.au)
Date: Fri May 13 2005 - 09:33:36 CDT

Dear VMDers,
I am using measure sasa to calculate buried surface area. To do this I am calculating the SA of two chains separately and together and the calculating the difference
set saA [measure sasa 1.4 $chainA]
set saB [measure sasa 1.4 $chainB]
set asAB [measure sasa 1.4 $chainAB]
set BuriedSurfaceArea [expr $saA + $saB - $saAB]

Does this look right?

When I do this I get some buried surface area even for chains that are not with 4 angstroms of each other???

I have used -samples 100

I have a large number of these measurement I wound rather not go through each one and draw points to check what is happening and then judiciously use -restrict $sel

Is there a better way of doing this? I am using sasa inappropriately?

Any help appreciated.

thanks

Matt