Amber

Introduction

Amber is a powerfull classical simulations package. It is not free, academic license costs $500. Ase-Amber has been tested only for amber16 (2016). It can bee usefull as MM part of QM/MM calculations since amber supports fast netCDF fileIO.

Water example

Generate topology file:

$ tleap -f tleap.in

where the tleap.in file contains:

source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
mol = loadpdb 2h2o.pdb
saveamberparm mol 2h2o.top h2o.inpcrd
quit

You need a file mm.in with instructions for the simulation:

zero step md to get energy and force
&cntrl
imin=0, nstlim=0,  ntx=1 !0 step md
cut=100, ntb=0,          !non-periodic
ntpr=1,ntwf=1,ntwe=1,ntwx=1 ! (output frequencies)
&end
END

Here is your example Python script:

from ase import Atoms
from ase.calculator.amber import Amber

atoms = Atoms('OH2OH2',
              [[-0.956, -0.121, 0],
               [-1.308, 0.770, 0],
               [0.000, 0.000, 0],
               [3.903, 0.000, 0],
               [4.215, -0.497, -0.759],
               [4.215, -0.497, 0.759]])

calc = Amber(amber_exe='sander -O ',
             infile='mm.in',
             outfile='mm.out',
             topologyfile='2h2o.top',
             incoordfile='mm.crd')
calc.write_coordinates(atoms, 'mm.crd')
atoms.set_calculator(calc)
f = atoms.get_forces()