[gmx-users] Protein ligand simulation

bharat gupta bharat.85.monu at gmail.com
Wed Apr 20 02:10:21 CEST 2016

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*

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