[gmx-users] Ligand observables in a protein-ligand simulation

[MUSYOKA THOMMAS]

I am trying to create an index file just as I did for the protein but am
lost when it comes to the following options

Keep 13 (this is ok as it is the ligand group number)

a -> Not sure since after trying CA or C i ended up getting the number of
atoms in the protein

name 13 Calpha (Not sure)

q

What options should I use for a and name 13 prompts?

Thank you


On Tue, Apr 15, 2014 at 12:12 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> The same way you'd do it for a protein, but with a suitable group.
>
> Mark
> On Apr 15, 2014 11:55 AM, "MUSYOKA THOMMAS" <mutemibiochemistry at gmail.com>
> wrote:
>
> > Dear Users,
> > How can one determine a ligand's rmsd, its radius of gyration, and its
> SASA
> > during a protein-ligand simulation?
> >
> > Thank you
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