RE: Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Oct 15 2018 - 10:35:25 CDT

Hi Rabeta,

How did the experimental group define "hydrophobic" and "hydrophillic"? Does it match with the VMD selection macro? I'd be surprised if it did. Also, have you checked what your "hydrophillic" selection comes back with? I think you will find that it isn't selecting what you think it is, since it also is selecting *anything* in your system that doesn't match the "hydrophobic" macro, which would include things like water and ions.

-Josh

On 2018-10-15 09:31:20-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

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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