VMD-L Mailing List

From: Anna Battisti (battistianna_at_googlemail.com)
Date: Tue Jan 31 2017 - 01:28:16 CST

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