• ## Outreach

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 31 2017 - 09:35:48 CST

This looks ok so far, but inside VMD you use the „-restrict“ flag to obtain the surface residue based. How do you do the same when using the external tool? So it’s reasonable you get different results.

Gesendet: Dienstag, 31. Januar 2017 12:31
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: vmd-l: SASA area

Sorry, what do you mean? maybe the flag I used?
./surf_LINUXAMD64 -W 1 -R 1.4 fort.1000

Anyway, step by steps, I have done the calculation in the following way:

1) starting from pdb file I generated the fort.1000 file:

awk 'BEGIN{while((getline < "output_VMDradius.dat")>0){n++; a[n]=\$1}}{printf "%4i%10.4f%10.4f%10.4f%10.4f\n",NR,a[NR],\$6,\$7,\$8}' temp2 > fort.1000

the beginning of the file is:

1 1.4000 31.3700 63.3600 63.0500
2 1.5000 32.1400 62.9100 61.8800
3 1.5000 31.2900 61.9600 61.0200
4 1.5000 32.1000 61.0600 60.1400
5 1.3000 30.4700 61.2400 61.9500
6 1.5000 32.6000 64.1100 61.0600
7 1.3000 31.9900 65.1700 61.1500
8 1.4000 33.6700 63.9300 60.2900
9 1.5000 34.2400 65.0600 59.5500
10 1.5000 35.6200 65.3500 60.1900
11 1.5000 36.6100 65.9800 59.2900
12 1.3000 35.4200 66.2000 61.3300
--------

The first column is the number of the line, the second is the VDW radius (calculated with VMD) then the coordinates (x, y, z)

2) Then I processed the fort.1000, and obtained fort.1000.tri in this way:

./surf_LINUXAMD64 -W 1 -R 1.4 fort.1000

3) I calculated the area of the triangles of the triangles.

Is this procedure correct?

On Tue, Jan 31, 2017 at 12:05 PM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

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> [mailto: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 <mailto: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