[gmx-users] really need some help with g_sas!!

[Mungikar, Amol Arvind (UMR-Student)]

hi, i ran g_sas only once and i got something like this: i have written what was what there 
It is actually written at the top of the output.xvg file.

  title "Solvent Accessible Surface"
  xaxis  label "Time (ps)"
  yaxis  label "Area (nm\S2\N)"
 TYPE xy
 view 0.15, 0.15, 0.75, 0.85
 legend on
 legend box on
 legend loctype view
 legend 0.78, 0.8
 legend length 2
 s0 legend "Hydrophobic"
 s1 legend "Hydrophilic"
 s2 legend "Total"
 s3 legend "D Gsolv"

1st column time (ps), 2nd hydrophobic sas (nm^2) ... etc.

I hope this helps a little!!
amol

	-----Original Message----- 
	From: gmx-users-admin at gromacs.org on behalf of Madhuri Agashe 
	Sent: Tue 2/17/2004 2:39 PM 
	To: gmx-users at gromacs.org 
	Cc: 
	Subject: [gmx-users] really need some help with g_sas!!
	
	

	Hi all,
	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)"
	
	What does the N in the unit stand for?
	
	Also 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??
	
	Has anyone used g_sas for this before???
	Please help!!
	
	Madhuri Agashe
	
	
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