rst-build-system

name	rst-build-system
description	Build simulation-ready molecular systems with rust_simulation_tools' SystemBuilder — load force fields, read PDB/mol2 structures, combine protein+ligand, solvate in explicit water, add counterions/salt, and write AMBER prmtop/inpcrd/PDB. Use for "build a system", "solvate", "add ions", "explicit/implicit solvent", "protein-ligand complex", or "write prmtop".

Building systems with SystemBuilder

SystemBuilder is a tleap-style system builder. The pattern is: create the builder, load force fields, load/combine structures into a System, optionally solvate and ionize, then write output. Methods that add solvent/ions mutate the System in place.

Force fields (load before loading structures)

builder = rst.SystemBuilder()
builder.load_protein_ff19sb()     # protein FF (ff19SB)
builder.load_gaff2()              # GAFF2 — needed for small-molecule ligands
builder.load_water_opc()          # OPC water model (for explicit solvent)
# Custom ligand parameters:
builder.load_custom_frcmod("ligand.frcmod")   # from parmchk2
builder.load_custom_lib("ligand.lib")         # custom residue library

Loading structures → System

protein = builder.load_pdb("protein.pdb")
ligand  = builder.load_mol2("ligand.mol2")     # pre-parameterized (GAFF2 + charges)
# Parameterize a raw ligand on the fly (runs antechamber internally):
ligand  = builder.load_ligand("ligand.sdf", net_charge=0)
system  = builder.combine([protein, ligand])

System exposes .n_atoms, .n_residues, .total_charge, .box_dimensions (None until solvated).

Solvation and ions

builder.solvate_box(system, buffer=12.0, closeness=1.0)   # rectangular OPC box

# count="neutralize" balances net charge; an int adds that many ions;
# a float is interpreted as a molar concentration.
builder.add_ions(system, "Na+", count="neutralize")  # returns number added
builder.add_ions(system, "Na+", count=20)            # 20 explicit Na+
builder.add_ions(system, "Cl-", count=0.150)         # 150 mM Cl-

Writing output

builder.write_amber(system, "system.prmtop", "system.inpcrd")  # both at once
builder.write_prmtop(system, "system.prmtop")                  # or individually
builder.write_inpcrd(system, "system.inpcrd")
builder.write_pdb(system, "system.pdb")

Workflows

• Implicit solvent (GB): load only load_protein_ff19sb(), load_pdb, then write prmtop/inpcrd. No solvation/ions — box_dimensions stays None.
• Explicit solvent: add load_water_opc(), solvate_box, then add_ions (neutralize, then excess salt), then write_amber.
• Protein-ligand complex: load protein + water + load_gaff2(), load custom frcmod/lib if needed, load_mol2/load_ligand, combine, solvate, ionize.

See examples/example_implicit_solvent.py, example_explicit_solvent.py, and example_protein_ligand.py. To generate ligand parameters first, see rst-parameterize-ligand.