VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 31 2017 - 05:05:52 CST

How did you tell the surf_LINUXAMD64 the restrict settings that you used in the TCL version?

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Anna Battisti
Gesendet: Dienstag, 31. Januar 2017 08:28
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: SASA area

 

Dear all,

 

I'm doing the sasa area calculation but something strange is happening: I'm seeing different results by comparing the calculation made with

 

set output [open "output_SASA.dat" w]

for {set x 0} {$x <= 2084} {incr x} {

set sel [atomselect top "index $x"]

set protein [atomselect top "protein"]

  set sasa [measure sasa 1.4 $protein -restrict $sel]

  puts $output "$sasa"

}

close $output

 

and that I obtained calculating the area of each atom as sum of the associated triangles area, when the triangles are obtained with:

 

./surf_LINUXAMD64 -W 1 -R 1.4 file > file.tri

 

I have supposed that the procedure to calculate the sasa with VMD is the same , namely surf_LINUXAMD64 is the VMD program.

 

Kindly, could you give me any kind of suggestion or tell me if there is some specific approximation?

 

Thanks

 

Anna