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

[Justin Lemkul]

On 1/16/18 7:46 AM, ZHANG Cheng wrote:
> Hi Justin,
> Thank you very much!
>
>
> The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded?

Strictly speaking, no, because you have artificial edges of that residue 
created by ignoring the fact that there are always residues flanking it. 
And you also have no guarantee that even in an "unfolded" state that 
this residue is 100% exposed to solvent. As an approximation, sure, but 
there is some level of error that may range from negligible to 
considerable, depending entirely upon the unfolded ensemble.

-Justin

>
> e.g.
> 1.467/2.767
> 1.824/2.757
> 1.901/2.736
> ... ...
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Tue, Jan 16, 2018 08:02 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.
>
>
> So I tried:
> gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1'
>
>
> And got:
>        0.000  206.865    1.467
>        0.100  232.450    1.824
>        0.200  225.984    1.901
>
>        ... ...
>
>
> So my understanding is
> ) 1st column is the time
> ) 2nd column is the sasa of the whole protein
> ) 3rd column is the sasa of the particular group
> Thank you for that.
>
>
> But may I ask
> 1) if it is possible to calculate the fraction for a particular group in this way:
> (sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
> Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually.
>
>
> 2) When I do not use -surface and -output, but use echo:
> echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns
>
>
> I got:
>        0.000    2.767
>        0.100    2.757
>        0.200    2.736
>
>        ... ...
>
>
> Do you know what is the meaning of the second column?
>
>
> Thank you!
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Tue, Jan 16, 2018 07:19 PM
> 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"?
>
>
>
> 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

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

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