Youtor
Molecular Dynamics Simulation of ProteinLigand using Gromacs
>> YOUR LINK HERE: ___ http://youtube.com/watch?v=hc8ZXbOMEfw
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: https://pubchem.ncbi.nlm.nih.gov/comp... • CHARMM Topology: http://mackerell.umaryland.edu/charmm... • #Latest #charmm36-jul2021.ff forcefield: http://mackerell.umaryland.edu/downlo... • #CGenff Server: https://cgenff.umaryland.edu/initguess/ • #CHARMM to GROMACS format: http://mackerell.umaryland.edu/downlo... • #sort_mol2_bonds.pl: http://www.mdtutorials.com/gmx/comple... • MDP files: • ions.mdp: http://www.mdtutorials.com/gmx/comple... • minim.mdp: http://www.mdtutorials.com/gmx/comple... • nvt.mdp: http://www.mdtutorials.com/gmx/comple... • npt.mdp:http://www.mdtutorials.com/gmx/comple... • md.mdp:http://www.mdtutorials.com/gmx/comple... • Github link: • https://github.com/pritampanda15/Mole... • 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. https://creativecommons.org/licenses/... • Source: http://incompetech.com/music/royalty-... • Artist: http://incompetech.com/ • #gromacs • #mdsimulation • #protein-ligand • #ligand • #charmm • #topology • #bioinformatics • #biophysics
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