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🎓 Featured Course Guide & Lesson Notes: Tutorial for Performing MM/GBSA and MM/PBSA free energy calculations from MD simulations with amber

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Instructor: In-Silico by Brandon Havranek  |  Runtime: 20:21 mins  |  Students / Views: 601,864

In this video I will show you a step by step tutorial for performing MM/GBSA and MM/PBSA relative free energy calculations from MD simulations using Amber/Ambertools. This tutorial assumes you have a basic understanding of how to run MD simulations. It is intended to showcase how to perform protein-ligand and protein-protein free energy calculations after simulation to find relative binding affinity values. If you found this tutorial helpful please like and subscribe. All commands used in this video: Input file for running PB and GB &general startframe=1500, endframe=3000, interval=60, strip_mask= :WAT:CLA:POT, / &gb igb=5, saltcon=0.150, / &pb istrng=0.150, inp=2, radiopt=0, prbrad=1.4, / ante-MMPBSA.py -p step3_input.parm7 -c com.prmtop -r rec.prmtop -l ligand.prmtop -s :WAT:CLA:POT -n :597-789 --radii mbondi2 MMPBSA.py -O -i mmpbsa.in -o resultsforwild.dat -sp step3_input.parm7 -cp com.prmtop -rp rec.prmtop -lp ligand.prmtop -y step5_production.nc Key Highlights & Overview: Understanding <strong>Amber Qm Mm Tutorial</strong> requires clear step-by-step guidance and practical hands-on visual demonstrations. Explore curated video courses, expert walkthroughs, and detailed lesson notes today on <strong>TutorTube</strong>.