Difference between revisions of "2024 AMBER tutorial 2 with PDBID 1NDV"
Stonybrook (talk | contribs) (→Introduction) |
Stonybrook (talk | contribs) (→Structure) |
||
Line 16: | Line 16: | ||
==Structure== | ==Structure== | ||
+ | We will need mol2 and pdb files of the ligand and receptor separately for these simulations. If you followed the 1NDV DOCK6 VS tutorial you will already have these files and can move them to the zzz.master directory, if not follow the steps below. Please note that the receptor file should be without charges and hydrogens, while the ligand will need the charges and hydrogens. | ||
+ | |||
+ | First open the PDB of 1NDV in Chimera. Now to select all the protein atoms we will | ||
==Force Field Parameters== | ==Force Field Parameters== |
Revision as of 20:09, 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.
Before Simulation
Structure
We will need mol2 and pdb files of the ligand and receptor separately for these simulations. If you followed the 1NDV DOCK6 VS tutorial you will already have these files and can move them to the zzz.master directory, if not follow the steps below. Please note that the receptor file should be without charges and hydrogens, while the ligand will need the charges and hydrogens.
First open the PDB of 1NDV in Chimera. Now to select all the protein atoms we will