Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Mon Oct 15 2018 - 10:26:45 CDT

Hi NAMD users,

I am trying to calculate hydrophobic and hydrophilic solvent accessible
surface area of a protein in a coarse grained system using VMD. I have used
a tcl script to do that. part of the tcl script is like this-
set sel [atomselect top protein]
set hydrophobic [atomselect top "hydrophobic"]
set sasa_phobic [measure sasa 1.4 $sel -restrict $hydrophobic]
set hydrophilic [atomselect top "not hydrophobic"]
set sasa_philic [measure sasa 1.4 $sel -restrict $hydrophilic]

It gives me much higher hydrophilic sasa than hydrophobic sasa. But
experimentally an also in others found that this protein should have higher
hydrophobic sasa compared to hydrophilic sasa.
Can anyone please help me how can I calculate those?

Thanks.
Rabeta Yeasmin

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