[gmx-users] Generate diagram/figure with information about protein-ligand interactions

[Tsjerk Wassenaar]

Hi biohpc,

For this you need to combine output from gmx hbond, gmx sasa, and gmx
saltbr.

Cheers,

Tsjerk
On Mar 31, 2016 12:58, "bio hpc" <biohpc2015 at gmail.com> wrote:

> My problem is not excel or whatever graphical program. I just need the
> data, in an automatic way. Then I can use either matplotlib or similar to
> get the plots automatically. But my question is if there is somewhere a
> repository of gromacs scripts with a script doing an analysis of the
> protein-ligand itneractions during trajectory. I do not think to be the
> only one requesting this
>
>
> > El 30/3/2016, a las 6:46, Sun Iba <sun.iba2 at gmail.com> escribió:
> >
> > i am sorry, i replied prior to looking at your figure. Actually, i have
> > never came across plotting data in this matter. However, I believe you
> have
> > tabulated data, so you can use Origin or excel for generating similar
> > images. You need little effort to arrange the data in desired manner.
> > Best Wishes
> >
> > On Wed, Mar 30, 2016 at 3:15 AM, bio hpc <biohpc2015 at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> after a protein-ligand simulation with gromacs, I would like to be able
> to
> >> generate a diagram/figure with information about protein-ligand
> >> interactions, something like this:
> >>
> >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
> >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
> >>
> >> I had a look to all gromacs tools but found nothing similar to this.
> Where
> >> can I start from?
> >>
> >> Thanks,
> >>
> >> biohpc
> >>
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