[gmx-users] g_sas (second column square of first)

[Craig Shepherd]

Hi there,

I meant to reply to this much earlier.  Some time ago,
someone emailed the list pointing out that the per-atom
SASA from g_sas had the square of the value in the first
column in the second column, instead of the standard deviation.

I had a look at the code, and it looks like this is the case.
I guess whoever just forgot to subtract the square of the averages
from the average of the squares.

So, just in case anyone needs to fix it quickly themselves, line
337 in g_sas.c:

fprintf(fp2,"%d %g %g\n",i+1,atom_area[index[i]]/j,
          atom_area2[index[i]]/j);

should be:

fprintf(fp2,"%d %g %g\n",i+1,atom_area[index[i]]/j,
          sqrt(atom_area2[index[i]]/j - 
((atom_area[index[i]]/j)*(atom_area[index[i]]/j))));

to get the std. dev. in your output.


Later,

Craig Shepherd