[gmx-users] Protein ligand simulation

[bharat gupta]

On Wed, Apr 20, 2016 at 12:03 PM, Terry <terrencesun at gmail.com> wrote:

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> Hi,
>
> If you mean you can not see the group with command `gmx make_ndx -f
> xxx.gro`, that's because you have not created one for it. Consult the
> manual for how to use make_ndx.
>
> Terry
>

Thanks Terry. I already discussed with Justin about this problem and now I
know where I was going wrong..

>
>
> On Wed, Apr 20, 2016 at 8:09 AM, bharat gupta <bharat.85.monu at gmail.com>
> wrote:
>
> > Dear Gmx users,
> >
> > I am performing a protein-ligand simulation using gromacs latest tutorial
> > for 5.0.x version. As per the tutorial, I included the coordinates of the
> > ligand in the complex.gro file (also updated total no. of atoms after
> > adding ligand atoms) and updated the topology file (topol.top) by
> including
> > its name under the molecules sections and also included its ligand.itp
> > file. But, I am not able to find the ligand group while making an index
> > file for it. Please let me know where am I going wrong ?
> >
> > --
> > *Best Regards*
> > BM
> > --
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