VMD-L Mailing List

From: Germán Andrés Miño (germino_at_u.uchile.cl)
Date: Mon Oct 22 2012 - 19:06:35 CDT

Hi VMD Users,

I would like to confirm if the units reported in the determination of
Solvent Accessible Surface Area (SASA) with VMD are squared Angstrom (A^2).

For the sasa calculation I´m using the following tcl script :

## Example script that sets the "User" data field with SASA values
##
mol delete all
mol addfile 1ap9.pdb

##
## Get list of residues
##
set allsel [atomselect top all]
set residlist [lsort -unique [$allsel get resid]]

##
## Make an atom selection, set the User field with the SASA value for
## the selected atom
##
foreach r $residlist {
  set sel [atomselect top "resid $r"]
  set rsasa [measure sasa 1.4 $allsel -restrict $sel]
  $sel set user $rsasa
  $sel delete
  puts "resdidue $r, sasa: $rsasa"
}

Thanks In advance

German Miño Galaz.
Postdoctoral Fellow of Grupo de Nanomateriales (www.gnm.cl)
Departamento de Fisica
Universidad de Chile.
Palmeras 3425, Nunoa.
Santiago Chile
Tel: 0056-2-978-7439
Fax: 0056-2-2712973