Engine for carrying out general purpose AMBER calculations. More...

Inheritance diagram for src.amberio.AMBER:

Collaboration diagram for src.amberio.AMBER:

Public Member Functions
def	__init__ (self, name="amber", kwargs)

def	setopts (self, kwargs)
	Called by init ; Set AMBER-specific options. More...

def	readsrc (self, kwargs)
	Called by init ; read files from the source directory. More...

def	callamber (self, command, stdin=None, print_to_screen=False, print_command=False, kwargs)
	Call AMBER; prepend amberhome to calling the appropriate ambertools program. More...

def	prepare (self, pbc=False, kwargs)
	Called by init ; prepare the temp directory and figure out the topology. More...

def	leap (self, read_prmtop=False, count_mols=False, name=None, delcheck=False)

def	get_charges (self)

def	evaluate_sander (self, leap=True, traj_fnm=None, snapshots=None)
	Utility function for computing energy and forces using AMBER. More...

def	energy_force_one (self, shot)
	Computes the energy and force using AMBER for one snapshot. More...

def	energy (self)
	Computes the energy using AMBER over a trajectory. More...

def	energy_force (self)
	Computes the energy and force using AMBER over a trajectory. More...

def	evaluate_cpptraj (self, leap=True, traj_fnm=None, potential=False)
	Use cpptraj to evaluate properties over a trajectory file. More...

def	kineticE_cpptraj (self, leap=False, traj_fnm=None)
	Evaluate the kinetic energy of each frame in a trajectory using cpptraj. More...

def	energy_dipole (self)
	Computes the energy and dipole using AMBER over a trajectory. More...

def	interaction_energy (self, fraga, fragb)
	Calculate the interaction energy for two fragments. More...

def	molecular_dynamics (self, nsteps, timestep, temperature=None, pressure=None, nequil=0, nsave=1000, minimize=True, anisotropic=False, threads=1, verbose=False, kwargs)
	Method for running a molecular dynamics simulation. More...

def	normal_modes (self, shot=0, optimize=True)

def	multipole_moments (self, shot=0, optimize=True, polarizability=False)

def	optimize (self, shot=0, method="newton", crit=1e-4)
	Optimize the geometry and align the optimized geometry to the starting geometry. More...

def	energy_rmsd (self, shot=0, optimize=True)
	Calculate energy of the selected structure (optionally minimize and return the minimized energy and RMSD). More...

Public Attributes
	valkwd
	Keyword args that aren't in this list are filtered out. More...

	amberhome

	have_pmemd_cuda

	spath

	leapcmd

	mdin

	absleap

	absmdin

	mname

	mol

	abspdb

	AtomLists

	pbc

	mol2

	frcmod

	absmol2

	absfrcmod

	qmatoms

	natoms

	AtomMask

	A

	B

	trajectory

Detailed Description

Engine for carrying out general purpose AMBER calculations.

Definition at line 1127 of file amberio.py.

Constructor & Destructor Documentation

◆ init()

def src.amberio.AMBER.__init__	(	self,
		name = `"amber"`,
		kwargs
	)

Definition at line 1130 of file amberio.py.

Member Function Documentation

◆ callamber()

def src.amberio.AMBER.callamber	(	self,
		command,
		stdin = `None`,
		print_to_screen = `False`,
		print_command = `False`,
		kwargs
	)

Call AMBER; prepend amberhome to calling the appropriate ambertools program.

Definition at line 1224 of file amberio.py.

◆ energy()

def src.amberio.AMBER.energy ( self )

Computes the energy using AMBER over a trajectory.

Definition at line 1459 of file amberio.py.

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◆ energy_dipole()

def src.amberio.AMBER.energy_dipole ( self )

Computes the energy and dipole using AMBER over a trajectory.

Definition at line 1561 of file amberio.py.

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◆ energy_force()

def src.amberio.AMBER.energy_force ( self )

Computes the energy and force using AMBER over a trajectory.

Definition at line 1464 of file amberio.py.

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◆ energy_force_one()

def src.amberio.AMBER.energy_force_one	(	self,
		shot
	)

Computes the energy and force using AMBER for one snapshot.

Definition at line 1453 of file amberio.py.

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◆ energy_rmsd()

def src.amberio.AMBER.energy_rmsd	(	self,
		shot = `0`,
		optimize = `True`
	)

Calculate energy of the selected structure (optionally minimize and return the minimized energy and RMSD).

In kcal/mol.

Definition at line 1830 of file amberio.py.

◆ evaluate_cpptraj()

def src.amberio.AMBER.evaluate_cpptraj	(	self,
		leap = `True`,
		traj_fnm = `None`,
		potential = `False`
	)

Use cpptraj to evaluate properties over a trajectory file.

Definition at line 1470 of file amberio.py.

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◆ evaluate_sander()

def src.amberio.AMBER.evaluate_sander	(	self,
		leap = `True`,
		traj_fnm = `None`,
		snapshots = `None`
	)

Utility function for computing energy and forces using AMBER.

Coordinates (and boxes, if pbc) are obtained from the Molecule object stored internally

Parameters

snapshots : None or list If a list is provided, only compute energies / forces for snapshots listed.

Outputs: Result: Dictionary containing energies and forces.

Definition at line 1374 of file amberio.py.

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◆ get_charges()

def src.amberio.AMBER.get_charges ( self )

Definition at line 1356 of file amberio.py.

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◆ interaction_energy()

def src.amberio.AMBER.interaction_energy	(	self,
		fraga,
		fragb
	)

Calculate the interaction energy for two fragments.

Definition at line 1567 of file amberio.py.

◆ kineticE_cpptraj()

def src.amberio.AMBER.kineticE_cpptraj	(	self,
		leap = `False`,
		traj_fnm = `None`
	)

Evaluate the kinetic energy of each frame in a trajectory using cpptraj.

This requires a netcdf-formatted trajectory containing velocities, which is generated using ntwv=-1 and ioutfm=1.

Definition at line 1534 of file amberio.py.

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◆ leap()

def src.amberio.AMBER.leap	(	self,
		read_prmtop = `False`,
		count_mols = `False`,
		name = `None`,
		delcheck = `False`
	)

Definition at line 1308 of file amberio.py.

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◆ molecular_dynamics()

def src.amberio.AMBER.molecular_dynamics	(	self,
		nsteps,
		timestep,
		temperature = `None`,
		pressure = `None`,
		nequil = `0`,
		nsave = `1000`,
		minimize = `True`,
		anisotropic = `False`,
		threads = `1`,
		verbose = `False`,
		kwargs
	)

Method for running a molecular dynamics simulation.

Required arguments: nsteps = (int) Number of total time steps timestep = (float) Time step in FEMTOSECONDS temperature = (float) Temperature control (Kelvin) pressure = (float) Pressure control (atmospheres) nequil = (int) Number of additional time steps at the beginning for equilibration nsave = (int) Step interval for saving and printing data minimize = (bool) Perform an energy minimization prior to dynamics threads = (int) Specify how many OpenMP threads to use

Returns simulation data: Rhos = (array) Density in kilogram m^-3 Potentials = (array) Potential energies Kinetics = (array) Kinetic energies Volumes = (array) Box volumes Dips = (3xN array) Dipole moments EComps = (dict) Energy components

Definition at line 1598 of file amberio.py.

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◆ multipole_moments()

def src.amberio.AMBER.multipole_moments	(	self,
		shot = `0`,
		optimize = `True`,
		polarizability = `False`
	)

Definition at line 1719 of file amberio.py.

◆ normal_modes()

def src.amberio.AMBER.normal_modes	(	self,
		shot = `0`,
		optimize = `True`
	)

Definition at line 1652 of file amberio.py.

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◆ optimize()

def src.amberio.AMBER.optimize	(	self,
		shot = `0`,
		method = `"newton"`,
		crit = `1e-4`
	)

Optimize the geometry and align the optimized geometry to the starting geometry.

Definition at line 1786 of file amberio.py.

◆ prepare()

def src.amberio.AMBER.prepare	(	self,
		pbc = `False`,
		kwargs
	)

Called by init ; prepare the temp directory and figure out the topology.

Definition at line 1238 of file amberio.py.

◆ readsrc()

def src.amberio.AMBER.readsrc	(	self,
		kwargs
	)

Called by init ; read files from the source directory.

Definition at line 1172 of file amberio.py.

◆ setopts()

def src.amberio.AMBER.setopts	(	self,
		kwargs
	)

Called by init ; Set AMBER-specific options.

Definition at line 1137 of file amberio.py.

Member Data Documentation

◆ A

src.amberio.AMBER.A

Definition at line 1570 of file amberio.py.

◆ absfrcmod

src.amberio.AMBER.absfrcmod

Definition at line 1280 of file amberio.py.

◆ absleap

src.amberio.AMBER.absleap

Definition at line 1177 of file amberio.py.

◆ absmdin

src.amberio.AMBER.absmdin

Definition at line 1179 of file amberio.py.

◆ absmol2

src.amberio.AMBER.absmol2

Definition at line 1275 of file amberio.py.

◆ abspdb

src.amberio.AMBER.abspdb

Definition at line 1215 of file amberio.py.

◆ amberhome

src.amberio.AMBER.amberhome

Definition at line 1141 of file amberio.py.

◆ AtomLists

src.amberio.AMBER.AtomLists

Definition at line 1241 of file amberio.py.

◆ AtomMask

src.amberio.AMBER.AtomMask

Definition at line 1336 of file amberio.py.

◆ B

src.amberio.AMBER.B

Definition at line 1571 of file amberio.py.

◆ frcmod

src.amberio.AMBER.frcmod

Definition at line 1245 of file amberio.py.

◆ have_pmemd_cuda

src.amberio.AMBER.have_pmemd_cuda

Definition at line 1151 of file amberio.py.

◆ leapcmd

src.amberio.AMBER.leapcmd

Definition at line 1175 of file amberio.py.

◆ mdin

src.amberio.AMBER.mdin

Definition at line 1176 of file amberio.py.

◆ mname

src.amberio.AMBER.mname

Definition at line 1182 of file amberio.py.

◆ mol

src.amberio.AMBER.mol

Definition at line 1197 of file amberio.py.

◆ mol2

src.amberio.AMBER.mol2

Definition at line 1244 of file amberio.py.

◆ natoms

src.amberio.AMBER.natoms

Definition at line 1328 of file amberio.py.

◆ pbc

src.amberio.AMBER.pbc

Definition at line 1242 of file amberio.py.

◆ qmatoms

src.amberio.AMBER.qmatoms

Definition at line 1296 of file amberio.py.

◆ spath

src.amberio.AMBER.spath

Definition at line 1164 of file amberio.py.

◆ trajectory

src.amberio.AMBER.trajectory

Definition at line 1639 of file amberio.py.

◆ valkwd

src.amberio.AMBER.valkwd

Keyword args that aren't in this list are filtered out.

Definition at line 1132 of file amberio.py.

The documentation for this class was generated from the following file:

amberio.py

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ callamber()

◆ energy()

◆ energy_dipole()

◆ energy_force()

◆ energy_force_one()

◆ energy_rmsd()

◆ evaluate_cpptraj()

◆ evaluate_sander()

Parameters

◆ get_charges()

◆ interaction_energy()

◆ kineticE_cpptraj()

◆ leap()

◆ molecular_dynamics()

◆ multipole_moments()

◆ normal_modes()

◆ optimize()

◆ prepare()

◆ readsrc()

◆ setopts()

Member Data Documentation

◆ A

◆ absfrcmod

◆ absleap

◆ absmdin

◆ absmol2

◆ abspdb

◆ amberhome

◆ AtomLists

◆ AtomMask

◆ B

◆ frcmod

◆ have_pmemd_cuda

◆ leapcmd

◆ mdin

◆ mname

◆ mol

◆ mol2

◆ natoms

◆ pbc

◆ qmatoms

◆ spath

◆ trajectory

◆ valkwd

◆ init()