[gmx-users] g_sas values of zero and Warning

[Nash, Anthony]

HI All,

I'm trying to get a measure of the solvent accessible surface area of a protein's catalytic site. It is unknown precisely how the substrate actually fits in the site given that in the crystal structure the site it too enclosed for the bulky substrate. I am using a progressive measure of g_sas -probe to get an idea of how accessible the catalytic site is during the simulation.

So I've tried six different -probe sizes, 0.1 (nm) 0.8, default , 1.6, 2.4, 3.2. Only in the first two instances do I actually get any read out. It appears as though I am unable to access the active site residues as the probe radius is near to a vdw radius. I could asume that the catalytic site is very enclosed, which could physiologically make sense. Or I have done something wrong, after all I am getting the warning:


WARNING: could not find a Van der Waals radius for 2 atoms
205 out of 205 atoms were classified as hydrophobic

Generated values per probe radius below:


-probe 0.1 (nm)
         0     8.30466           0     8.30466
       100     8.04708           0     8.04708
       200     7.82871           0     7.82871
.....

DEFAULT: -probe       real   0.14    Radius of the solvent probe (nm)
         0     4.30913           0     4.30913
       100     4.24779           0     4.24779
       200     3.81957           0     3.81957

-probe 0.8 (nm)
         0           0           0           0
       100           0           0           0
       200           0           0           0
......

-probe 1.6 (nm)
         0           0           0           0
       100           0           0           0
       200           0           0           0
......

-probe 2.4
         0           0           0           0
       100           0           0           0
       200           0           0           0
....

-probe 3.2
         0           0           0           0
       100           0           0           0
       200           0           0           0

Many thanks
Anthony