Molecular Dynamics Simulation of Protein-Ligand using Gromacs

This tutorial will guide a new user through the process of setting up a simulation system containing a protein Mpro-SARS-CoV-2 in complex with a ligand (Nirmatrelvir). This tutorial focuses specifically on issues related to dealing with the ligand, assuming that the user is familiar with basic GROMACS operations and the contents of a topology.
#Ligand: pubchem.ncbi.n...
CHARMM Topology: mackerell.umary...
#Latest #charmm36-jul2021.ff forcefield: mackerell.umary...
#CGenff Server: cgenff.umaryla...
#CHARMM to GROMACS format: mackerell.umary...
#sort_mol2_bonds.pl: www.mdtutorials...
MDP files:
ions.mdp: www.mdtutorials...
minim.mdp: www.mdtutorials...
nvt.mdp: www.mdtutorials...
npt.mdp:www.mdtutorials...
md.mdp:www.mdtutorials...
Github link:
github.com/pri...
Notes:
The ion names have been updated to SOD for NA and CLA for CL.
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname SOD -nname CLA -neutral
For updated coordinate numbers in topol.top: highest number - lowest number / 3
Music
Almost in F - Tranquillity by Kevin MacLeod is licensed under a Creative Commons Attribution 4.0 license. creativecommon...
Source: incompetech.com...
Artist: incompetech.com/
#gromacs
#mdsimulation
#protein-ligand
#ligand
#charmm
#topology
#bioinformatics
#biophysics