# How to visualize protein-ligand complex MD run using VMD

GROMACS version: gmx, version 2021.4 GROMACS modification: No

I'm following the Protein-Ligand Complex tutorial. I'd like to visualize the binding using VMD.

I use the output from these commands:

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr

gmx mdrun -deffnm md_0_10


Especially these two files:

md_0_10.gro
md_0_10.xtc


And with this VMD setting:

At best I can get is only the receptor (protein) but not the ligand bound to it. This is done by assigning "protein" to Selected Atoms form in Graphical Representation dialog box. I can't see anything where I can include ligand.

How can I also show ligand in the binding?

• Is your ligand already with protein or no ? Do u have a PDB file or no ? Dec 20, 2021 at 10:28
• @Abd-ElazeemMohamed Yes. Already with protein. Dec 20, 2021 at 12:02
• Do u just want to show the ligand with the protein ? Dec 20, 2021 at 12:06
• @Abd-ElazeemMohamed Yes. Just ligand with the protein. Dec 21, 2021 at 3:18