Difference between revisions of "2024 AMBER tutorial 2 with PDBID 1NDV"
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=Introduction= | =Introduction= | ||
| + | DOCK6 is a great tool that helps us understand ligand binding poses and relative binding energies. When DOCK6 is combined with another computational method known as molecular dynamics, we can calculate free energies of binding and probe how the ligand behaves in the binding pocket. In this tutorial we will walk through the use of AMBER16 to perform and analyze molecular dynamic simulations of PDBID 1NDV. | ||
==Getting Started== | ==Getting Started== | ||
| + | Before starting simulations it is important to create our directories so that we can keep our simulations organized. Create the following directories: | ||
| + | 000.paramters | ||
| + | 001.tleap_build | ||
| + | 002.equilbration | ||
| + | 003.production | ||
| + | 004.analysis | ||
| + | zzz.master | ||
| + | |||
| + | We will use the zzz.master directory to store our initial mol2 files and other files we may use that do not belong in another directory. Once you have your directories created you can begin to prepare they system for simulation. | ||
=Before Simulation= | =Before Simulation= | ||
Revision as of 19:57, 5 May 2024
Contents
Introduction
DOCK6 is a great tool that helps us understand ligand binding poses and relative binding energies. When DOCK6 is combined with another computational method known as molecular dynamics, we can calculate free energies of binding and probe how the ligand behaves in the binding pocket. In this tutorial we will walk through the use of AMBER16 to perform and analyze molecular dynamic simulations of PDBID 1NDV.
Getting Started
Before starting simulations it is important to create our directories so that we can keep our simulations organized. Create the following directories:
000.paramters 001.tleap_build 002.equilbration 003.production 004.analysis zzz.master
We will use the zzz.master directory to store our initial mol2 files and other files we may use that do not belong in another directory. Once you have your directories created you can begin to prepare they system for simulation.
