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

[Sun Iba]

The figure is generated using Desmond. Check the following paper:

http://dx.doi.org/10.1016/j.bmc.2014.02.020

On Thu, Mar 31, 2016 at 4:34 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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