[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[ZHANG Cheng]

Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  Can I get the fraction of solvent accessible surface area using "gmx sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue.


Thank you.


Yours sincerely
Cheng