System Setup with tLEaP

Assembling the Enzyme-Ligand-Solvent System

Building the Solvated System with tLEaP

Use the tLEap input file included in this tutorial for building a “matured” MD input system.

We are going to use:

  • leaprc.protein.ff19SB for the protein

  • leaprc.gaff2 for the ligand molecule

  • leaprc.water.spce for the water molecules

Building with tLEap
tleap -f 2-tleap.in

Here is the content of the tutorial/metadata/system/2-tleap.in

Load, combine, solvate, neutralise and finally build a ready to simulate system
# Sourcing required force-field parameters for protein, ligand and water
source leaprc.protein.ff19SB
source leaprc.gaff2
source leaprc.water.spce

# Load protein structure (Use the protonated PDB)
protein = loadPDB tutorial/metadata/input_structures/wt_protein.pdb
check protein

# Load flavins parameters and structure
loadamberparams tutorial/metadata/ff/FMH/gaff2/FMH.frcmod
loadoff tutorial/metadata/ff/FMH/gaff2/FMH.lib
fmn = loadpdb tutorial/metadata/input_structures/FMH.pdb
check fmn

# Load Ligand parameters and structure
loadamberparams tutorial/metadata/ff/OHP/gaff2/OHP.frcmod
loadoff tutorial/metadata/ff/OHP/gaff2/OHP.lib
OHP = loadpdb tutorial/metadata/input_structures/OHP.pdb
check OHP

# Saving unsolvated dry system's pdb and parameter file
system = combine {protein fmn OHP}
savepdb system tutorial/metadata/system/xenA_h_OHP_dry.pdb
saveamberparm system tutorial/metadata/system/xenA_h_OHP_dry.prmtop tutorial/metadata/system/xenA_h_OHP_dry.rst7

# Solvate using a preconfigured water model box
solvateOct system SPCBOX 10 iso

# Neutralise by adding counter ions
addions2 system Cl- 0
addions2 system Na+ 0

# Save AMBER input files for solvated and neutralised system
savePDB system tutorial/metadata/system/xenA_h_OHP.pdb
saveamberparm system tutorial/metadata/system/xenA_h_OHP.parm7 tutorial/metadata/system/xenA_h_OHP.rst7
quit

Here is the final system, we just built

_images/system_v2.png

The final fully “matured” system. Its a octahedral box, where water molecules shown as transparent surface, protein in gray cartoon, ions in light blue, flavin and OHP in yellow and cyan, respectively.