Difference between revisions of "2023 AMBER tutorial 2 with PDBID 3WZE"

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(Directory Setup)
Line 5: Line 5:
  
 
== '''Directory Setup''' ==
 
== '''Directory Setup''' ==
 
+
As always, we set up folders to keep us organized as we move generate files:
 
+
mkdir 001_structure
 +
mkdir 002_parameters
 +
mkdir 003_leap
 +
mkdir 004_equil
 +
mkdir 005_production
  
 
== '''3WZE Structures''' ==
 
== '''3WZE Structures''' ==

Revision as of 15:45, 5 May 2023

Introduction

Directory Setup

As always, we set up folders to keep us organized as we move generate files:

mkdir 001_structure
mkdir 002_parameters
mkdir 003_leap
mkdir 004_equil
mkdir 005_production

3WZE Structures

Receptor

Ligand

Amber Simulation Parameters

Tleap

Equilibration

Production

MD Analysis

RMSD

Hydrogen Bonding

MM-GBSA