How to visualize protein-ligand complex MD run using VMD

Question

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?

Answer 1

First, You need to click on Create Rep and you will get a new line in the box below as the picture attached (with the same name "protein" in your case).

To show the ligand, you should know the name of your ligand, to ensure about your ligand name, you can choose in the keyword "resname" and all the resname will appear in the value box. Or you can see the number of residue of your ligand , if you have the pdb file, you can know the number of the residue easily

Then select one of the two line in the box under Create Rep and start to write the name of your ligand in selected atom section Like this resname LIG or this resid 41

Last thing, you can change the draw style of your ligand, so you can see clearly and observe if there is binding or reaction etc