Saturday, November 22, 2014

Computing a solvent accessible surface area using Jmol

Someone asked me how to compute a surface area of a molecule.  Here's how to compute a solvent accessible surface area using Jmol.

1. Load your molecule into Jmol (File > Open)

2. Open the Script Editor and Output Console (File > Script Editor, etc)

3. Type the following three lines into the Script Editor window and hit run

set solventproberadius 1.2
isosurface solvent
isosurface area set 0

1.2 Å is the probe radius for water solvent.  If you are using another solvent input another value.  It will correspond roughly to the radius of the solvent molecule.

4. The are will be printed out in the Console.  The units are not specified but I'm sure it's Å2 (square Ångstrom)

1 comment:

Anonymous said...

Thanks for your guide. However I faced with a problem. I found SAS of 2,4-pentanedion in PM3 level inside water (with 1.4 angstrom radius) 304.08 (A2) in literature (Orlando Tapia, Solvent Effects and Chemical Reactivity). However, when I open the optimized structure in Jmol, I found 123.81811 (A2) which is very different. What is the Problem?