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.. module:: ase.calculators.amber
Amber
=====
Introduction
------------
Amber_ is a powerful classical simulations package. It is not free, academic
license costs $500. Ase-Amber has been tested only for amber16 (2016). It can
bee useful as MM part of QM/MM calculations since amber supports fast netCDF
fileIO.
.. _Amber: http://ambermd.org
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.calculators.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.calc = calc
f = atoms.get_forces()
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