VMD-L Mailing List

From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Wed Apr 03 2013 - 11:07:38 CDT

Dear all,

I have been having some problems with a quite simple task. I want to
measure the buried surface of a complex. For that i created the
following script

proc complexSasa { complex partner1 } {
     set asaPartner1Free [ measure sasa 1.4 $partner1 ]
     set asaPartner1Complex [ measure sasa 1.4 $complex -restrict
$partner1 ]
     set complexArea [ expr $asaPartner1Free - $asaPartner1Complex ]
     return $complexArea
}

This basically measures how much of the area of the molecule is hidden
upon complexation. In principle, it should give the same result using
either one of the partners of the complex. However, i am getting
significantly different results.

For instance for for the barnase barstar complex using the following

mol new 2za4

set complex [ atomselect top "protein and chain A B"]
set chainA [ atomselect top "protein and chain A"]
set chainB [ atomselect top "protein and chain B"]

complexSasa $complex $chainA
754.0234375

complexSasa $complex $chainB
719.96435546875

So the difference is quite considerable.

Any ideas where this difference comes from? It is likely that i am
making a mistake.

Regards

Felipe