2023 AMBER tutorial 2 with PDBID 3WZE

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

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