[gmx-users] Data generated by g_sas

[mon_sharma at research.iiit.ac.in]

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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