def test_PME_QMMM(self):
# compare to saved test: PME + QMMM
topfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/inpcrd")
traj = pt.load(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
options.ifqnt = 1
options.jfastw = 4
qm_options = sander.QmInputOptions()
qm_options.qm_theory = "PDDG-PM3"
qm_options.qmmask = ":1-2"
qm_options.qmcharge = 0
qm_options.scfconv = 1e-10
qmmm_tight_p_conv = 1
qm_options.qmmm_int = 5
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 605.7349, tol=3E-4)
assert_close(edict['vdw_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec'][0], -7409.7167, tol=3E-1)
assert_close(edict['scf'][0], -37.1277, tol=3E-4)
def minimize(parm, igb, saltcon, cutoff, tol, maxcyc):
""" Minimizes a snapshot. Use the existing System if it exists """
if not HAS_SANDER:
raise SimulationError('Could not import sander')
if not HAS_SCIPY:
raise SimulationError('Could not import scipy')
if parm.box is None:
if not igb in (0, 1, 2, 5, 6, 7, 8):
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, '
'6, 7, or 8')
if cutoff is None: cutoff = 999.0
inp = sander.gas_input(igb)
inp.saltcon = saltcon
inp.cut = cutoff
else:
if cutoff is None: cutoff = 8.0
inp = sander.pme_input()
inp.cut = cutoff
# Define the objective function to minimize
def energy_function(xyz):
sander.set_positions(xyz)
e, f = sander.energy_forces()
return e.tot, -np.array(f)
with sander.setup(parm, parm.coordinates, parm.box, inp):
options = dict(maxiter=maxcyc, disp=True, gtol=tol)
results = optimize.minimize(energy_function, parm.coordinates,
method='L-BFGS-B', jac=True,
options=options)
parm.coordinates = results.x
if not results.success:
print('Problem minimizing structure with scipy and sander:',
file=sys.stderr)
print('\t' + results.message)
def test_PME_QMMM(self):
# compare to saved test: PME + QMMM
topfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/inpcrd")
traj = pt.load(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
options.ifqnt = 1
options.jfastw = 4
qm_options = sander.QmInputOptions()
qm_options.qm_theory = "PDDG-PM3"
qm_options.qmmask = ":1-2"
qm_options.qmcharge = 0
qm_options.scfconv = 1e-10
qmmm_tight_p_conv = 1
qm_options.qmmm_int = 5
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 605.7349, tol=3E-4)
assert_close(edict['vdw_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec'][0], -7409.7167, tol=3E-1)
assert_close(edict['scf'][0], -37.1277, tol=3E-4)
def minimize(parm, igb, saltcon, cutoff, tol, maxcyc, disp=True, callback=None):
""" Minimizes a snapshot. Use the existing System if it exists """
if not HAS_SANDER:
raise SimulationError('Could not import sander')
if not HAS_SCIPY:
raise SimulationError('Could not import scipy')
if parm.box is None:
if not igb in {0, 1, 2, 5, 6, 7, 8}:
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, 6, 7, or 8')
if cutoff is None: cutoff = 999.0
inp = sander.gas_input(igb)
inp.saltcon = saltcon
inp.cut = cutoff
else:
if cutoff is None: cutoff = 8.0
inp = sander.pme_input()
inp.cut = cutoff
# Define the objective function to minimize
def energy_function(xyz):
sander.set_positions(xyz)
e, f = sander.energy_forces()
return e.tot, -np.array(f)
with sander.setup(parm, parm.coordinates, parm.box, inp):
options = dict(maxiter=maxcyc, disp=disp, gtol=tol)
more_options = dict()
if callable(callback):
more_options['callback'] = callback
results = optimize.minimize(energy_function, parm.coordinates, method='L-BFGS-B', jac=True,
options=options, **more_options)
parm.coordinates = results.x
if not results.success:
LOGGER.error(f'Problem minimizing structure with scipy and sander: {results.message}')
def test_PME(self):
# compare to saved test: PME
topfile = os.path.join(amberhome, "test/4096wat/prmtop")
rstfile = os.path.join(amberhome, "test/4096wat/eq1.x")
traj = pt.iterload(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
edict = pt.energy_decomposition(traj=traj, mm_options=options)
assert_close(edict['bond'][0], 0., tol=3E-4)
assert_close(edict['vdw'][0], 6028.9517, tol=3E-4)
assert_close(edict['elec'][0], -45371.5995, tol=3E-4)
def test_PME(self):
# compare to saved test: PME
topfile = os.path.join(amberhome, "test/4096wat/prmtop")
rstfile = os.path.join(amberhome, "test/4096wat/eq1.x")
traj = pt.iterload(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
edict = pt.energy_decomposition(traj=traj, mm_options=options)
assert_close(edict['bond'][0], 0., tol=3E-4)
assert_close(edict['vdw'][0], 6028.9517, tol=3E-4)
assert_close(edict['elec'][0], -45371.5995, tol=3E-4)
def sanderforce(self,parmstr,atmlst,boxflag=False,pmeflag=False):
"""Calculates energy and forces for a provided
Amber parm string and set of coordinates using the Sander
API. Also takes box dimensions and a flag for use of PME.
Currently uses standard simulation options for gas phase or pme
based on pmeflag.
Only returns forces on first 2 atoms in atmlst
Returns a sander energy object and a 3 x 2 x traj length array
of forces with units"""
self.forces=[]
self.energies=[]
# sander.APPLY_UNITS = True # More bugs/inconsistencies in pysander in amber15, may be fixed later
indices = [a.idx for a in atmlst[:2]]
if pmeflag is True:
# These default options will be suitable in most cases
# PME,cut=8.0,ntb=1,ntf=1,ntc=1
# Should be adapted if shake is required (not important here for ele)
inp = sander.pme_input()
else:
inp = sander.gas_input()
for i in range(0,self.traj.frame):
coord = self.traj.coordinates[i]
if boxflag is True:
box = self.traj.box[i]
# print box
else:
box = None
with sander.setup(parmstr,coord,box=box,mm_options=inp): #Pass a string, else a temp parmfile is created that fills up tmp directory!
ene,frc = sander.energy_forces(as_numpy=False) # pysander __init__ bug/inconsistency, can't use as_numpy!
frc = np.asarray(frc)
frc = np.reshape(frc,((len(frc)/3.),3))
frcslice = frc[indices]
# Add units for forces: kcal mol-1 A-1
frcslice = frcslice * u.kilocalorie / (u.mole * u.angstroms)
self.forces.append(frcslice)
self.energies.append(ene)
def test_eneregy_and_force():
path = os.path.dirname(__file__)
prmtop = path + '/vAla3.prmtop'
rst7 = path + '/vAla3.rst7'
with mdgx.setup(prmtop, rst7) as context:
mdgx_energies, mdgx_forces = context.energy_forces()
pme_input = sander.pme_input()
parm = pmd.load_file(prmtop, rst7)
with sander.setup(prmtop, rst7, box=parm.box, mm_options=pme_input):
ene, sander_forces = sander.energy_forces()
sander_enegies = dict((att, getattr(ene, att)) for att in dir(ene) if not
att.startswith('_'))
print("")
print("potential energy")
print("sander_enegies")
print(sander_enegies['tot'])
print("mdgx_energies")
print(mdgx_energies['eptot'])
print("")
print('forces')
print('sander_forces, first 5 atoms')
print(sander_forces[:15])
print("")
print('mdgx_forces, first 5 atoms')
print(mdgx_forces.tolist()[:15])
aa_eq([sander_enegies['tot'],],
[mdgx_energies['eptot'],],
decimal=4)
group.add_argument('--cutoff',
dest='cutoff',
type=float,
default=8,
help='''Cutoff for nonbonded forces in Angstroms. Cutoff is
always infinite for non-periodic systems''')
group.add_argument('--platform',
dest='platform',
default='Reference',
help='OpenMM platform to use. Default is %(default)s')
args = parser.parse_args()
# Get the Amber forces and energies
if args.pbc:
inp = sander.pme_input()
inp.cut = args.cutoff
inp.ntc = inp.ntf = 1
else:
inp = sander.gas_input(args.igb)
inp.cut = 1000
inp.rgbmax = 1000
with sander.setup(args.prmtop, args.inpcrd, None, inp) as context:
e, f = sander.energy_forces()
f = np.array(f).reshape((context.natom, 3))
# Get the OpenMM forces and energies
parm = app.AmberPrmtopFile(args.prmtop)
inpcrd = app.AmberInpcrdFile(args.inpcrd)
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np
pdb = '3stl'
parm = AmberParm('4amber_%s.prmtop' % pdb) #topo
rst = Rst7.open('4amber_%s.rst7' % pdb) #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)
import code
code.interact(local=dict(globals(), **locals()))
sander.cleanup()
def energy(parm, args, output=sys.stdout):
"""
Compute a single-point energy using sander and print the result to the
desired output
Parameters
----------
parm : Structure
args : ArgumentList
output : file handler, default sys.stdout
"""
global HAS_SANDER
if not HAS_SANDER:
raise SimulationError('Could not import sander')
cutoff = args.get_key_float('cutoff', None)
igb = args.get_key_int('igb', 5)
saltcon = args.get_key_float('saltcon', 0.0)
do_ewald = args.has_key('Ewald')
vdw_longrange = not args.has_key('nodisper')
has_1264 = 'LENNARD_JONES_CCOEF' in parm.parm_data
# Get any unmarked arguments
unmarked_cmds = args.unmarked()
if len(unmarked_cmds) > 0:
warnings.warn("Un-handled arguments: " + ' '.join(unmarked_cmds),
UnhandledArgumentWarning)
if parm.ptr('ifbox') == 0:
if not igb in (0, 1, 2, 5, 6, 7, 8):
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, '
'6, 7, or 8')
# Force vacuum electrostatics down the GB code path
if igb == 0:
igb = 6
inp = sander.gas_input(igb)
if cutoff is None:
cutoff = 1000.0
if cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
if saltcon < 0:
raise SimulationError('salt concentration must be >= 0')
inp.saltcon = saltcon
elif parm.ptr('ifbox') > 0:
inp = sander.pme_input()
if cutoff is None:
cutoff = 8.0
elif cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
inp.ew_type = int(do_ewald)
inp.vdwmeth = int(vdw_longrange)
inp.lj1264 = int(has_1264)
if parm.coordinates is None:
raise SimulationError('No coordinates are loaded')
# Time to set up sander
with sander.setup(parm, parm.coordinates, parm.box, inp):
e, f = sander.energy_forces()
if parm.chamber:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f Urey-Bradley = %20.7f\n'
'Improper = %20.7f ' %
(e.bond, e.angle, e.dihedral, e.angle_ub, e.imp))
if parm.has_cmap:
output.write('CMAP = %20.7f\n' % e.cmap)
output.write('1-4 vdW = %20.7f 1-4 Elec. = %20.7f\n'
'Lennard-Jones = %20.7f Electrostatic = %20.7f\n'
'TOTAL = %20.7f\n' %
(e.vdw_14, e.elec_14, e.vdw, e.elec, e.tot))
else:
output.write(
'Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f 1-4 vdW = %20.7f\n'
'1-4 Elec = %20.7f vdWaals = %20.7f\n'
'Elec. = %20.7f' %
(e.bond, e.angle, e.dihedral, e.vdw_14, e.elec_14, e.vdw, e.elec))
if igb != 0 and inp.ntb == 0:
output.write(' Egb = %20.7f' % e.gb)
elif e.hbond != 0:
output.write(' EHbond = %20.7f' % e.hbond)
output.write('\nTOTAL = %20.7f\n' % e.tot)
def energy(parm, args, output=sys.stdout):
"""
Compute a single-point energy using sander and print the result to the
desired output
"""
global HAS_SANDER
if not HAS_SANDER:
raise SimulationError('Could not import sander')
cutoff = args.get_key_float('cutoff', None)
igb = args.get_key_int('igb', 5)
saltcon = args.get_key_float('saltcon', 0.0)
do_ewald = args.has_key('Ewald')
vdw_longrange = not args.has_key('nodisper')
has_1264 = 'LENNARD_JONES_CCOEF' in parm.parm_data
# Get any unmarked arguments
unmarked_cmds = args.unmarked()
if len(unmarked_cmds) > 0:
warnings.warn("Un-handled arguments: " + ' '.join(unmarked_cmds),
UnhandledArgumentWarning)
if parm.ptr('ifbox') == 0:
if not igb in (0, 1, 2, 5, 6, 7, 8):
raise SimulationError('Bad igb value. Must be 0, 1, 2, 5, '
'6, 7, or 8')
# Force vacuum electrostatics down the GB code path
if igb == 0:
igb = 6
inp = sander.gas_input(igb)
if cutoff is None:
cutoff = 1000.0
if cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
if saltcon < 0:
raise SimulationError('salt concentration must be >= 0')
inp.saltcon = saltcon
elif parm.ptr('ifbox') > 0:
inp = sander.pme_input()
if cutoff is None:
cutoff = 8.0
elif cutoff <= 0:
raise SimulationError('cutoff must be > 0')
inp.cut = cutoff
inp.ew_type = int(do_ewald)
inp.vdwmeth = int(vdw_longrange)
inp.lj1264 = int(has_1264)
if parm.coordinates is None:
raise SimulationError('No coordinates are loaded')
# Time to set up sander
with sander.setup(parm, parm.coordinates, parm.box, inp):
e, f = sander.energy_forces()
if parm.chamber:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f Urey-Bradley = %20.7f\n'
'Improper = %20.7f ' % (e.bond, e.angle,
e.dihedral, e.angle_ub, e.imp))
if parm.has_cmap:
output.write('CMAP = %20.7f\n' % e.cmap)
output.write('1-4 vdW = %20.7f 1-4 Elec. = %20.7f\n'
'Lennard-Jones = %20.7f Electrostatic = %20.7f\n'
'TOTAL = %20.7f\n' % (e.vdw_14, e.elec_14,
e.vdw, e.elec, e.tot))
else:
output.write('Bond = %20.7f Angle = %20.7f\n'
'Dihedral = %20.7f 1-4 vdW = %20.7f\n'
'1-4 Elec = %20.7f vdWaals = %20.7f\n'
'Elec. = %20.7f' % (e.bond, e.angle, e.dihedral,
e.vdw_14, e.elec_14, e.vdw, e.elec))
if igb != 0 and inp.ntb == 0:
output.write(' Egb = %20.7f' % e.gb)
elif e.hbond != 0:
output.write(' EHbond = %20.7f' % e.hbond)
output.write('\nTOTAL = %20.7f\n' % e.tot)
import sander
from parmed.amber.readparm import AmberParm, Rst7
import numpy as np
import os, sys
import pickle
base = '1nie'
# parm = AmberParm('4amber_%s.prmtop' %base) #topo
rst = Rst7.open('4amber_%s.rst7' %base) #box
coords1 = rst.coordinates
coords2 = np.around( np.array(pickle.load(open('tmp2','rb') ) ), 3) #2nd coordinate set
print coords1, coords1.shape
print coords2, coords2.shape
sander.setup('4amber_%s.prmtop' %base, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print frc[0]
sander.set_positions(coords1)
ene, frc = sander.energy_forces()
print frc[0]
sander.set_positions(coords2)
ene, frc = sander.energy_forces()
print frc[0]
print max(frc)
print ene.tot, ene.elec, ene.vdw
# import code; code.interact(local=dict(globals(), **locals()))
import boost.python
group.add_argument('--pbc', dest='pbc', default=False, action='store_true',
help='Specify the use of periodic boundary conditions')
group.add_argument('-g', '--igb', dest='igb', default=0, type=int,
help='''GB model to use (see Amber manual). Default is
%(default)s''')
group.add_argument('--cutoff', dest='cutoff', type=float, default=8,
help='''Cutoff for nonbonded forces in Angstroms. Cutoff is
always infinite for non-periodic systems''')
group.add_argument('--platform', dest='platform', default='Reference',
help='OpenMM platform to use. Default is %(default)s')
args = parser.parse_args()
# Get the Amber forces and energies
if args.pbc:
inp = sander.pme_input()
inp.cut = args.cutoff
else:
inp = sander.gas_input(args.igb)
inp.cut = 1000
with sander.setup(args.prmtop, args.inpcrd, None, inp) as context:
e, f = sander.energy_forces()
f = np.array(f).reshape((context.natom, 3))
# Get the OpenMM forces and energies
parm = app.AmberPrmtopFile(args.prmtop)
inpcrd = app.AmberInpcrdFile(args.inpcrd)
gbmap = collections.defaultdict(lambda: None)
gbmap[1] = app.HCT
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np
pdb ='3stl'
parm = AmberParm('4amber_%s.prmtop' %pdb) #topo
rst = Rst7.open('4amber_%s.rst7' %pdb) #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)
import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()
#! /usr/bin/env python
import sander
from chemistry.amber.readparm import AmberParm, Rst7
from chemistry.structure import Structure, read_PDB, write_PDB
import numpy as np
parm = AmberParm('4amber_1cby.prmtop')
pdb = read_PDB('new.pdb')
rst = Rst7.open('4amber_1cby.rst7')
xyz = pdb.pdbxyz[0]
sander.setup(parm,xyz, rst.box, sander.pme_input())
sander.set_positions(xyz)
ene, frc = sander.energy_forces()
#~ import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()
