pysander_restraint.py

import sander
import parmed

options = sander.pme_input()
options.cut = 8.0
options.ntr = 1
options.refc = '../ubiquitin/inpcrd'
options.restraintmask = '!:WAT'
options.restraint_wt = 1.

rst = parmed.load_file('../ubiquitin/inpcrd')
with sander.setup("../ubiquitin/prmtop", rst.coordinates, rst.box, options):
    e, f = sander.energy_forces()
    print(e.tot)