GROMACS version:2022.5
GROMACS modification: No
Hi,
I am new to MD Simulations in Gromacs specially the Protein-Ligand complex in a POPC membrane. I have done a 100 ns simulation and now would like to analyze the data. I was going through the analysis part in the Membrane Protein: KALP15 in DPPC simulation tutorial provided on the Gromacs Website. However, I could not find the information that I am looking for. Specifically, I am looking for the following basic kind of analysis: rmsd of protein, rmsd of ligand, distances between protein and ligand, H-Bond analysis between protein and ligand etc.
So I am planning on following the steps and commands mentioned on protein-ligand complex simulation tutorial. I will begin with centering my trajectory (Choose “Protein” for centering and “System” for output) and then perform rotational and translational fitting (Choose “Backbone” to perform least-squares fitting to the protein backbone, and “System” for output). Then going for the routine RMSD, RMSF, H-BONDs, and distances measurement analysis.
I am looking for an expert advice on how should I proceed. Whether my above described approach is correct or needs any additional modifications that I am missing out.
Many thanks in advance