def cleanup_amber(self):
if self.sander and self.amber_structs:
if self.amber_structs.is_LES:
import sanderles
sanderles.cleanup()
else:
import sander
sander.cleanup()
def cleanup(self):
make_header('Cleaning up - Amber')
if self.sander and self.amber_structs:
if self.amber_structs.is_LES:
import sanderles
sanderles.cleanup()
else:
import sander
sander.cleanup()
def get_total_energy(agls):
# get the coor from pyrosetta
inp_coor=generate_coord(agls)
# initialize the object topology with coordinates
parm=AmberParm("tpp-1.prmtop",inp_coor)
# set up the input options
inp=sander.gas_input()
sander.setup (parm, parm.coordinates, None, inp)
# compute the energy and force
eney, frc=sander.energy_forces()
# print('sander',eney.tot,eney.gb,eney.vdw, eney.elec, eney.dihedral,eney.angle, eney.bond)
# clean and finish
sander.cleanup()
return eney.tot
#! /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()
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 sander.set_positions(rst.coordinates) 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 sander.cleanup()
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)
gbmeth, kappa = None, 0.0
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 not hasattr(parm, 'coords'):
raise SimulationError('No coordinates are loaded')
# Time to set up sander
sander.setup(parm, parm.coords, 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)
sander.cleanup()
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)
gbmeth, kappa = None, 0.0
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 not hasattr(parm, 'coords'):
raise SimulationError('No coordinates are loaded')
# Time to set up sander
sander.setup(parm, parm.coords, 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)
sander.cleanup()
