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:
[EMAIL PROTECTED] 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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