Amber Wrapper

class esteem.wrappers.amber.AmberWrapper(nprocs=None)

Sets up the AMBER Calculator (via ASE) for Molecular Dynamics runs

prepare_input_acpype(seed, netcharge=0, offset=0)

Prepares input parameters and topologies for Amber calculations

prepare_input(seed, netcharge=0, offset=0)

Prepares input parameters and topologies for Amber calculations

add_solvent_box(solute, solvent, counterions, solvatedseed, box_size)

Loads an Amber mol2 file for a solute and solvent, and creates a solvated box

reimage(seed, infile, outfile)

Runs the cpptraj program with a simple script to center the frame on residue 1 (the solute) and translate molecules back into the home cell

dipole(seed, crdfile)

Runs the cpptraj program with a simple script to get the dipole moment from the final trajectory

fix_amber_pdb(seed)

An awk-based hack to fix AMBER pdb files to make them work with ASE

singlepoint(model, seed, calc_params={}, forces=False, solvent=None, readonly=False, continuation=False)

Runs a singlepoint calculation with the Amber ASE calculator

geom_opt(model, seed, calc_params={}, solvent=None)

Runs a geometry optimisation calculation with the Amber ASE calculator

heatup(model, seed, calc_params={}, nsteps=100)

Runs a heatup temperature-ramp calculation with the Amber ASE calculator

densityequil(model, seed, calc_params={}, nsteps=100)

Runs a density equilibration calculation with fixed hydrogens with the Amber ASE calculator

equil(model, seed, calc_params={}, nsteps=100)

Runs an equilibration calculation at constant volume with flexible hydrogens with the Amber ASE calculator

snapshots(model, seed, calc_params={}, nsnaps=1, nsteps=100, start=0)

Runs a long MD trajectory for snapshot generation with the Amber ASE calculator