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

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(Directory Setup)
(Amber Simulation Parameters)
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=='''Amber Simulation Parameters'''==
 
=='''Amber Simulation Parameters'''==
 
+
To generate parameters for the simulation, we must implement the following:
 +
antechamber -i ../001_structure/3wze_lig_wH.mol2 -fi mol2 -o 3wze_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 0
 +
nc = 0 because the charge on the ligand is 0. If your ligand is non-zero, enter the appropriate charge at the end of this line. It may be helpful to check the protonation state of the ligand at pH 7.
 +
Once 3wze_ligand_antechamber.mol2 output file is generated, run parmch2:
 +
parmchk2 -i 3wze_ligand_antechamber.mol2 -f mol2 -o 3wze_ligand.am1bcc.frcmod
  
 
=='''Tleap'''==
 
=='''Tleap'''==

Revision as of 15:49, 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

To generate parameters for the simulation, we must implement the following:

antechamber -i ../001_structure/3wze_lig_wH.mol2 -fi mol2 -o 3wze_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 0

nc = 0 because the charge on the ligand is 0. If your ligand is non-zero, enter the appropriate charge at the end of this line. It may be helpful to check the protonation state of the ligand at pH 7. Once 3wze_ligand_antechamber.mol2 output file is generated, run parmch2:

parmchk2 -i 3wze_ligand_antechamber.mol2 -f mol2 -o 3wze_ligand.am1bcc.frcmod

Tleap

Equilibration

Production

MD Analysis

RMSD

Hydrogen Bonding

MM-GBSA