Difference between revisions of "2022 AMBER tutorial 1 with PDBID 6ME2"
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== '''Using TLeap''' == | == '''Using TLeap''' == | ||
| + | Now, switch to the following directory: | ||
| + | |||
| + | cd 003_leap | ||
| + | |||
| + | Where files will be generated to simulate the ligand and receptor, such that further calculations involving both structures--such as binding affinities, free energies, and trajectories. Two types of files will be generated that can be used to set up the system: parameter ('''parm7''') and restart ('''rst7''') files. Start the process by creating the following input file: | ||
| + | |||
| + | vi leap.in | ||
| + | |||
| + | And put the following into the input file: | ||
| + | |||
| + | #!/usr/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 ../001_structure/6me2_fresh.pdb | ||
| + | ###load ligand frcmod/mol2 | ||
| + | loadamberparams ../002_parameters/6me2_ligand.am1bcc.frcmod | ||
| + | lig=loadmol2 ../002_parameters/1HW9_ligand_antechamber.mol2 | ||
| + | ###create gase-phase complex | ||
| + | gascomplex= combine {rec lig} | ||
| + | ###write gas-phase pdb | ||
| + | savepdb gascomplex 6me2.gas.complex.pdb | ||
| + | ###write gase-phase toplogy and coord files for MMGBSA calc | ||
| + | saveamberparm gascomplex 6me2.complex.parm7 6me2.gas.complex.rst7 | ||
| + | saveamberparm rec 6me2.gas.receptor.parm7 6me2.gas.receptor.rst7 | ||
| + | saveamberparm lig 6me2.gas.ligand.parm7 6me2.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 6me2.wet.complex.pdb | ||
| + | ###check the system | ||
| + | charge solvcomplex | ||
| + | check solvcomplex | ||
| + | ###write solvated toplogy and coordinate file | ||
| + | saveamberparm solvcomplex 6me2.wet.complex.parm7 6me2.wet.complex.rst7 | ||
| + | quit | ||
== '''Equilibrating the system''' == | == '''Equilibrating the system''' == | ||
Revision as of 16:30, 3 May 2022
Contents
Introduction
AMBER is a program designed for computing biomolecular simulations. In this tutorial, AMBER will be used to simulate the dynamics between the ligand and receptor of the 6ME2 PDB file.
Directory Setup
For this tutorial, it is recommended to define the following directories to stay organized:
mkdir 001_structure mkdir 002_parameters mkdir 003_leap mkdir 004_equil mkdir 005_production
6ME2 Structure Files
If the 6ME2 DOCK tutorials were followed before this AMBER tutorial, the user has some experience generating and prepping receptor and ligand filed from the original 6ME2 PDB file. However, it is recommended that the user NOT use the files generated in the 6ME2 DOCK tutorials and to instead start from scratch here, as this allows the chance to catch mistakes that may have been made but not recognized while following the initial DOCK tutorials.
To begin this tutorial, search the Protein Data Bank (PDB) website using the code 6ME2, or use the Fetch... button on the home screen of UCSF Chimera for this four-letter code. All the following structures should be saved to the following directory:
cd 001_structure
Receptor File Generation
To generate a fresh copy of the receptor file, open the 6me2.pdb file containing the ligand-receptor complex. Go to
Select -> Structure -> protein
which will select the receptor, and then go to
Select -> Invert (all models)
to select everything other than the receptor in the file. Then, go to
Actions -> Atoms/Bonds -> delete
which will isolate the receptor. Go to
File -> Save Mol2...
and save as 6me2_rec.mol2. Close Chimera.
Ligand File Generation
To generate the ligand file, open the 6me2.pdb file again, and go to
Select -> Structure -> protein
then
Actions -> Atoms/Bonds -> delete
to delete the receptor. Then, go to
Select -> Residue -> HOH -> Actions -> Atoms/Bonds -> delete
Select -> Residue -> OLA -> Actions -> Atoms/Bonds -> delete
Select -> Residue -> PEG -> Actions -> Atoms/Bonds -> delete
to delete everything except for the JEV residue, which is the ligand of interest here.
Note: there are problems with the file containing the ligand as-is. In order to proceed properly, it is necessary to make some changes to this file. While the file is still open, go to
Tools > Structure Editing > Rotamers
and change the non-standard YCM residue to the most probable rotamers of CYS.
After this is completed, go to
Tools > Structure editing > Add H
to add hydrogens to the ligand. Then, go to
Tools > Structure editing > Add Charge > (have Amber ff14SB and AM1-BCC selected) -> Ok
and then go to
File -> Save Mol2...
and save as 6me2_lig_dockprep.mol2. Close Chimera.
Generating Simulation Parameters
In order to generate parameters for this tutorial, switch to the following directory:
cd 002_parameters
To generate the parameters, run the following command:
antechamber -i ../001_structure/6me2_lig_wH.mol2 -fi mol2 -o 6me2_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 0
Note the -nc flag is set to 0 in the above line; this should correspond to the protonation state of the ligand. If a user is following this tutorial to simulate dynamics on a structure other than 6ME2, be sure to double check and change this value accordingly.
After the 6me2_ligand_antechamber.mol2 output file is generated, run the following command to run parmch2:
parmchk2 -i 6me2_ligand_antechamber.mol2 -f mol2 -o 6me2_ligand.am1bcc.frcmod
Using TLeap
Now, switch to the following directory:
cd 003_leap
Where files will be generated to simulate the ligand and receptor, such that further calculations involving both structures--such as binding affinities, free energies, and trajectories. Two types of files will be generated that can be used to set up the system: parameter (parm7) and restart (rst7) files. Start the process by creating the following input file:
vi leap.in
And put the following into the input file:
#!/usr/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 ../001_structure/6me2_fresh.pdb
###load ligand frcmod/mol2
loadamberparams ../002_parameters/6me2_ligand.am1bcc.frcmod
lig=loadmol2 ../002_parameters/1HW9_ligand_antechamber.mol2
###create gase-phase complex
gascomplex= combine {rec lig}
###write gas-phase pdb
savepdb gascomplex 6me2.gas.complex.pdb
###write gase-phase toplogy and coord files for MMGBSA calc
saveamberparm gascomplex 6me2.complex.parm7 6me2.gas.complex.rst7
saveamberparm rec 6me2.gas.receptor.parm7 6me2.gas.receptor.rst7
saveamberparm lig 6me2.gas.ligand.parm7 6me2.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 6me2.wet.complex.pdb
###check the system
charge solvcomplex
check solvcomplex
###write solvated toplogy and coordinate file
saveamberparm solvcomplex 6me2.wet.complex.parm7 6me2.wet.complex.rst7
quit
