[gmx-users] Protein-Ligand Interaction calculation

[Bratin Kumar Das]

Hi..
      You have to specify energy groups in .mdp option..then rerun the
simulation..and analyse with gmx energy command

On Mon 17 Feb, 2020, 5:52 PM Александр Лашков, <alashkov83 at gmail.com> wrote:

> You can rebuild index file using gmx make_ndx gromacs util.
> Alex
>
> пн, 17 февр. 2020 г. в 15:19, Peter Mawanga <peter.mawanga.lagos at gmail.com
> >:
>
> > Hello everyone
> >
> > I used the CHARMM-GUI Membrane Builder to build a bilayer around my
> > protein-ligand complex.
> >
> > However, unfortunately the ligand was not mentioned separately in the
> index
> > (.ndx) file although it was mentioned in the topology (.top) file. Hence
> I
> > am not able to calculate the energy between the protein and ligand using
> > the energy (.edr) file.
> >
> > Please let me know if there is any workaround for this. It would be
> > difficult to repeat the simulations again.
> >
> >
> > --
> > Cheers
> > Peter
> > --
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