Difference between revisions of "2023 AMBER tutorial 2 with PDBID 3WZE"
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parmchk2 -i 3wze_ligand_antechamber.mol2 -f mol2 -o 3wze_ligand.am1bcc.frcmod | 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 | ||
=='''Equilibration'''== | =='''Equilibration'''== |
Revision as of 15:56, 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
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