VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Mar 10 2008 - 14:41:08 CDT

Hi all,

I've been trying to calculate the total and hydrophobic
solvent-accessible surface area from a few trajectories I have.
Everything works well, except for a single detail: when I calculate
the hydrophobic and hydrophilic part of the SASA, the sum of both over
the trajectory doesn't match at all the value I get when I calculate
the total SASA. Do you have any idea of what could be wrong? For the
calculation of the total SASA I'm using "atomselect top protein"; for
the hydrophobic "atomselect top "protein and hydrophobic" and for the
hydrophilic "atomselect top protein and not hydrophobic".

I remember that this topic was discussed before, but I just can't find
that specific post in the list. All comments will be appreciated!

Cheers,
Michel