[gmx-users] gmx sasa output confusion

[Teemu Murtola]

That was also part of the bug fix: with the fixed version, you should get
the same number of rows and the same areas on each row, but the first
column will have the correct residue numbers.

Teemu

On Thu, Nov 5, 2015, 19:12 Francesco Carbone <fra.carbone8 at gmail.com> wrote:

> 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 ?
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>