[gmx-users] problems with the outpur for g_sas

Madhuri Agashe magashe at CLEMSON.EDU
Mon Feb 16 01:24:01 CET 2004


I have a protein fragment which has a chain of 13 residues. I am interested
in finding the changes in solvent accessible area before and after running a
MD run on it.
I ran the g_sas command with the -or option.
The header for the xvg output file says @ title "Area per residue", xaxis
label "Residue" and yaxis  label "Area (nm\S2\N)"

The output in the .xvg file created looks like this:
1	0.276705	0.279141
2	0.361234	0.362187
3	0.330778	0.332667
4	0.25564	0.257268
5	0.398971	0.399676
6	0.373965	0.376628
7	0.465398	0.466495
8	0.27801	0.279602
9	0.235051	0.236743
10	0.16984	0.172215
11	0.149311	0.151239
12	0.0597569	0.0681734
13	0.121558	0.124841
14	0.0709042	0.0762016
15	0.166491	0.171072
16	0.294642	0.298024
17	0.368115	0.368736
18	0.197868	0.200265
19	0.337358	0.338604
	0	4.63489

how do I interpret this? 
Is the first column for time?? What I have shown here is only the beginning
of the .xvg file. It has such values for all 13 residues.

Any suggestions???

Thanks,
Madhuri





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