[gmx-users] gmx sasa output confusion

[Francesco Carbone]

Thank you for your reply,
Everything makes sens, the only thing that I still haven't understood is
the reason for which I have multiple lines for the residues.
Are those atoms? then why are there, if I want the single residue?

Regards,

Fra

On 5 November 2015 at 16:33, Teemu Murtola <teemu.murtola at gmail.com> wrote:

> Hi,
>
> The issue with incorrect legends and X axis has been fixed in 5.0.6.
>
> As for the four columns, you are asking gmx sasa to calculate the same
> numbers twice, so you get them twice: according to gmx sasa -h, the area of
> -surface selection is always calculated, and -output (which is optional)
> just specifies extra groups on top of this to calculate the area for.
>
> As for the legends for the extra columns, no one has just had the time to
> implement nice output for all possible cases.
>
> Best regards,
> Teemu
>
> On Wed, Nov 4, 2015 at 7:20 PM Francesco Carbone <fra.carbone8 at gmail.com>
> wrote:
>
> > Good afternoon,
> > I calculated the residue area (-or) over my trajectory, but I have
> trouble
> > understanding the output.
> >
> > With gromacs 4.6 I obtain a clean file:
> >
> >       residue   value       standard dev
> >         27     4.65478    1.19505
> >         28    0.990566   0.966795
> >         29     1.77202   0.629798
> >         30    0.389708   0.374724
> >         31           0          0
> >         32           0          0
> >         33           0          0
> >         34           0          0
> >
> > with gromacs 5 instead I see odd things:
> >
> > 1) the titles between -or and -oa results are swapped.
> > -or gives "title "Area per atom over the trajectory"", while -oa "title
> > "Area per residue over the trajectory"".
> > xaxis is set correct (res with -or and atom with -oa)
> >
> > 2)  I have 18 times the same residues plus 4 columns with only s0 and s1
> > with legend ("Average" and "Standard dev")
> >
> > I'm using this command:
> >
> > gmx sasa -s file.tpr -f file.xtc -n file.ndx -or ciao5.xvg -surface
> Protein
> > -output Protein -dt 5000
> >
> > Is there some changes I have missed ?
> >
> --
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