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

[ZHANG Cheng]

Hi Alexandr,
Thank you, but it is the same with spaces between | 
:(


Cheng




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

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



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is output". 
) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
  Near '1'
    syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
  Near '0'
    syntax error



Can you please help me? Thank you very much!
------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

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



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