[gmx-users] Data generated by g_sas

[Tsjerk Wassenaar]

Monika,

Daniel has already given the answer. The third column gives the
standard deviation, whereas the second gives the average SAS. You
could've found this answer also by browsing the mailing list archive,
as this is one of those questions being posted every once in a
while...

Cheers,

Tsjerk

On Thu, Mar 6, 2008 at 8:58 AM,  <mon_sharma at research.iiit.ac.in> wrote:
> Hello All,
>  For reference, the output files are as:
>
>  # This file was created Thu Jan 31 17:27:21 2008
>  # by the following command:
>  # g_sas -f pro-total-21ns-300K-PT.xtc -s pro-3ns-300K-PT.tpr -o
>  pro-21ns-300K-g_sas-area.xvg -or pro-21ns-300K-g_sas-resarea.xvg -oa
>  pro-21ns-300K-g_sas-atomarea.xvg -q pro-21ns-300K-g_sas-connelly.xvg
>  #
>  # g_sas is part of G R O M A C S:
>  #
>  # Gromacs Runs One Microsecond At Cannonball Speeds
>  #
>  @    title "Area per residue"
>  @    xaxis  label "Residue"
>  @    yaxis  label "Area (nm\S2\N)"
>  @TYPE xy
>           1    0.867478   0.178453
>           2     1.05816   0.248229
>           3     1.12171   0.280894
>           4     1.54811   0.212061
>           5    0.532166   0.119596
>           6     2.05678   0.271594
>           7     1.43324    0.18675
>           8      0.9919   0.156349
>           9    0.745497   0.277242
>          10    0.193999  0.0824625
>          11    0.573983   0.238295
>          12    0.934204  0.0959199
>          13    0.671052   0.143626
>          14     0.15924  0.0966806
>          15     1.14398    0.19238
>          16     1.32751   0.240461
>          17    0.594131   0.169421
>          18    0.256019   0.150048
>          19     1.24637   0.251035
>          20     1.18673    0.13117
>          21    0.734073   0.147444
>          22     1.22901   0.169386
>          23     0.30032   0.137402
>          24     1.17923   0.222947
>          25     0.52457    0.18227
>          26    0.564586   0.198732
>  This is an excerpt from the output file
>  for g_sas area calculation per residue.
>
>  Thanking you,
>  Regards,
>  Monika
>
>  On
>  Thu, 6 Mar 2008, Mark Abraham wrote:
>
>  > mon_sharma at research.iiit.ac.in wrote:
>  >> Hello All,
>  >> This might sound a bit stupid question. But I have no idea about it. So
>  >> here I am asking it.
>  >> I am using g_sas to calculate the solvent accessible area. But I am not
>  >> able to understand the values the program is giving out. I am using options
>  >> -or and -oa to get it plotted per residue and atom.  It generates three
>  >> columns data per residue-type and atom-type output. First column for
>  >> Residue# or atom#. I am confused what the second and third columns
>  >> corresponds to? If anyone can suggest me. There are no legends provided in
>  >> the xvgr file generated either.
>  >
>  > Providing a sample of parts of the output files would be a useful thing to
>  > do.
>  >
>  > Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623