Post-Processing of Protein-Ligand Simulation in GROMACS

In this detailed video, we explore the post-processing analyses of GROMACS protein-ligand complex, focusing on key metrics such as Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Solvent Accessible Surface Area (SASA), hydrogen bonding (H-Bonds), and interaction energy. Watch as we break down each analysis method, demonstrate how to perform these calculations, and interpret the results to better understand the protein-ligand interactions. Perfect for researchers, students, and enthusiasts in molecular dynamics and computational biology.
This tutorial will guide a new user through the process of setting up a simulation system containing a protein in complex with a ligand . 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....
Tutorial link: www.mdtutorials...
#gromacs
#mdsimulation
#proteinligand
#ligand
#charmm
#topology
#bioinformatics
#biophysics
#post-processing
#HydrogenBondAnalysis, #HBonds, #InteractionEnergy, #MolecularDynamics, #ComputationalBiology, #PostProcessingAnalysis, #ProteinStructureAnalysis, #Bioinformatics, #DrugDiscovery, #ProteinInteraction, #ProteinDocking, #LigandBinding, #MolecularModeling, #StructuralBioinformatics, #ProteinFlexibility, #DynamicSimulation, #ProteinDynamics, #MolecularInteraction, #BindingAffinity, #ProteinAnalysisTools, #StructuralAnalysis, #ComputationalChemistry, #SimulationTools, #StructuralDynamics, #ProteinConformation, #DrugDesign, #ProteinLigandBinding, #MolecularSimulationAnalysis, #ProteinBehavior, #ComputationalDrugDiscovery
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