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