GROMACS version: 22.04
GROMACS modification: Yes/No
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" Finally, we may be interested in quantifying how much the ligand binding pose has changed over the course of the simulation. To compute a heavy-atom RMSD of just JZ4, create a new index group for it:
gmx make_ndx -f em.gro -n index.ndx
…
13 & ! a H*
name 26 JZ4_Heavy
q
Execute the rms module, choosing “Backbone” for least-squares fitting and “JZ4_Heavy” for the RMSD calculation. By doing so, the overall rotation and translation of the protein is removed via fitting and the RMSD reported is how much the JZ4 position has varied relative to the protein, which is a good indicator of how well the binding pose was preserved during the simulation.
gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_jz4.xvg
The calculated RMSD should be about 0.1 nm (1 Å), indicating only a very small change in the ligand’s position. "
The above statement pertains to the protein-ligand tutorial.
My goal is to calculate the binding free energy using the third-party tool gmx_MMPBSA.
First, I plan to identify a stable region (in my 100 ns simulation, 2000 frame) of the protein-ligand complex based on the RMSD. After determining the stable region, I will use that specific frame for the calculation.
Q1 : If I want to calculate the RMSD of the protein-ligand complex, should I use the gmx make_ndx -f em.gro -n index.ndx command to create an index group for the protein-ligand complex, and then choose “backbone” for least-squares fitting and “the complex we created earlier” for the RMSD calculation?
As a first-time user of GROMACS, I am always receiving a lot of help in the forums.