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

[Justin Lemkul]

On 1/16/18 6:19 AM, ZHANG Cheng wrote:
> Hi Alexandr,
> Thank you, but it is the same with spaces between |
> :(

I provided the appropriate syntax before:

http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas

-select and -output take strings that select what you want for each. Do 
that, not echo.

-Justin

>
> 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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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