[gmx-users] Protein ligand simulation

Terry terrencesun at gmail.com
Wed Apr 20 05:03:45 CEST 2016


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.


On Wed, Apr 20, 2016 at 8:09 AM, bharat gupta <bharat.85.monu at gmail.com>

> 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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