VMD-L Mailing List

From: henri mone (henrimone_at_gmail.com)
Date: Thu Jul 01 2010 - 17:19:06 CDT

Dear VMD users,

I'm using the "sasa" command in VMD to calculate the hydrophobic and
hydrophilic surface of my system.
I'm using the commands sequence as reported in [1].
I have following questions:

1. I found several different algorithms to calculate the SASA. Which
SASA algorithm is implemented in VMD. Can someone point me to the
corresponding paper.

2. Which exact definition of hydrophobic and hydrophilic does VMD use?
Can someone point me to the corresponding paper/ description.

3. To select the hydrophilic atoms I use the command "set phil
[atomselect top 'not hydrophobic']". Does the selection "not
hydrophobic" really select only the hydrophilic atoms or are some
additional atoms (e.g. neutral atoms) selected? If additional neutral
atoms are selected, how can I restrict the selection to only the
hydrophilic atoms?

Thank you
Hneri