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

Revision as of 15:59, 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

Next we will generate the AMBER topology file and coordinate files. Switch to the directory:

vi leap.in

Two types of files will be generated, parm7 (topology) and rst7 (coordinates). Create the input file:

vi leap.in

And then input the following (make sure you change the username):

   #!/USERNAME/bin/sh 
   ###load protein force field
   source leaprc.protein.ff14SB
   ###load GAFF force field (for our ligand)
   source leaprc.gaff
   ###load TIP3P (water) force field
   source leaprc.water.tip3p
   ###load ions frcmod for the tip3p model 
   loadamberparams frcmod.ionsjc_tip3p
   ###needed so we can use igb=8 model 
   set default PBradii mbondi3
   ###load protein pdb file 
   rec=loadpdb ../000_structure/3wze_rec.pdb
   ##@make disulfide bond
   ###load ligand frcmod/mol2
   loadamberparams ../000_structure/3wze_ligand.am1bcc.frcmod  
   lig=loadmol2 ../000_structure/3wze_ligand_antechamber.mol2
   ###create gase-phase complex
   gascomplex= combine {rec lig}
   ###write gas-phase pdb
   savepdb gascomplex 3wze.gas.complex.pdb
   ###write gas-phase toplogy and coord files for MMGBSA calc
   saveamberparm gascomplex 3wze.complex.parm7 3wze.gas.complex.rst7
   saveamberparm rec 3wze.gas.receptor.parm7 3wze.gas.receptor.rst7
   saveamberparm lig 3wze.gas.ligand.parm7 3wze.gas.ligand.rst7
   ###create solvated complex (albeit redundant)
   solvcomplex= combine {rec lig}
   ###solvate the system
   solvateoct solvcomplex TIP3PBOX 12.0
   ###Neutralize system
   addions solvcomplex Cl- 0
   addions solvcomplex Na+ 0
   #write solvated pdb file
   savepdb solvcomplex 3wze.wet.complex.pdb
   ###check the system
   charge solvcomplex 
   check solvcomplex
   ###write solvated toplogy and coordinate file
   saveamberparm solvcomplex 3wze.wet.complex.parm7 3wze.wet.complex.rst7
   quit

Once the files are generated, transfer the parm7 and rst7 files to the local environment. You can run them in Chimera to check the build. Open the protein, then open TOOLS--MD/ENSEMBLE ANALYSIS--MD MOVIE. Open the parm7 in prmtop box and then add the rst7 as a trajectory. Then click OK.

Equilibration

Production

MD Analysis

RMSD

Hydrogen Bonding

MM-GBSA