VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Jun 06 2019 - 11:05:15 CDT

Hi Daeun,

Measuring SASA in VMD can be done through the scripting interface, specifically the "measure sasa" command (http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html). I think you'd want to do something like this:

#Select the whole protein
set psel [atomselect top "protein"]
#Select only the part you care about. I encourage you to visualize both of these selections.
set ressel [atomselect top "sidechain and protein and resid 1"]

for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
$psel frame $f
$ressel frame $f
puts "Frame $f: SASA = [measure sasa 1.4 $psel -restrict $ressel]
}

-Josh

On 2019-06-05 17:38:38-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Hello all,
I am a new VMD user and now I am struggling with the program.
I am trying to do SASA calculation of my peptide.
Specifically, I'd like to see the SASA for the side chains of the specific residue not whole residue in my peptide structure but I don't know how to type commands.
Are there any ways or commands to specify atom numbers to select only side chains and measure the SASA?
thank you!
Sincerely,
Daeun