Post-Processing of Protein-Ligand Simulation in GROMACS

Описание: 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: 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...

Tutorial link: http://www.mdtutorials.com/gmx/

#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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