def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB'))
)
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
def test_write_xml_parameters_charmm_multisite_waters(self):
""" Test writing XML parameter files from Charmm multisite water parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(
get_fn('toppar_water_ions_tip5p.str')))
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='toppar_water_ions_tip5p.str',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
# Check that water has the right number of bonds
assert len(
params.residues['TIP5'].bonds
) == 2, "TIP5P should only have two bonds, but instead has {}".format(
params.residues['TIP5'].bonds)
# Parameterize water box
pdbfile = app.PDBFile(get_fn('waterbox.pdb'))
modeller = app.Modeller(pdbfile.topology, pdbfile.positions)
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.NoCutoff)
# Parameterize water box
pdbfile = app.PDBFile(get_fn('waterbox-tip3p.pdb'))
modeller = app.Modeller(pdbfile.topology, pdbfile.positions)
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=app.PME)
def test_write_xml_small_amber(self):
""" Test writing small XML modifications """
params = openmm.OpenMMParameterSet.from_parameterset(
load_file(os.path.join(get_fn('parm'), 'frcmod.constph')))
ffxml_filename = get_fn('test.xml', written=True)
params.write(ffxml_filename)
forcefield = app.ForceField(ffxml_filename)
def test_write_xml_parameters_methanol_ions_energy(self):
""" Test writing XML parameter files from Charmm parameter files, reading them back into OpenMM ForceField, and computing energy of methanol and NaCl """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_cgenff.prm'),
get_fn('top_all36_cgenff.rtf'),
get_fn('toppar_water_ions.str')) # WARNING: contains duplicate water templates
)
del params.residues['TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_cgenff.prm, top_all36_cgenff.rtf, toppar_water_ions.str',
Reference='MacKerrell'
)
)
forcefield = app.ForceField(ffxml_filename)
# Parameterize methanol and ions in vacuum
pdbfile = app.PDBFile(get_fn('methanol_ions.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
ffxml_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Compute energy via ParmEd reader
psf = CharmmPsfFile(get_fn('methanol_ions.psf'))
system = psf.createSystem(params)
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
parmed_potential = context.getState(getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Ensure potentials are almost equal
self.assertAlmostEqual(ffxml_potential, parmed_potential)
def test_write_xml_parameters_charmm(self):
""" Test writing XML parameter files from Charmm parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf'),
get_fn('toppar_water_ions.str')) # WARNING: contains duplicate water templates
)
del params.residues['TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm, top_all36_prot.rtf',
Reference='MacKerrell'
)
)
forcefield = app.ForceField(ffxml_filename)
# Check that water has the right number of bonds
assert len(params.residues['TIP3'].bonds) == 2, "TIP3P should only have two bonds"
# Parameterize alanine tripeptide in vacuum
pdbfile = app.PDBFile(get_fn('ala_ala_ala.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
# Parameterize ACE-NME in water
pdbfile = app.PDBFile(get_fn('2igd_924wat.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.PME)
def test_write_xml_parameters_charmm(self):
""" Test writing XML parameter files from Charmm parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf'),
get_fn('toppar_water_ions.str')))
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm, top_all36_prot.rtf',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB')))
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2179)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1647)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p')))
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml, write_unused=True)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
# Load TIP3P water box to ensure there are no duplicate ion parameters
pdbfile = app.PDBFile(get_fn('ionsjc.pdb'))
system = forcefield.createSystem(pdbfile.topology)
def test_explicit_improper(self):
""" Test writing out the improper explicitly and reading it back into OpenMM ForceField """
warnings.filterwarnings('ignore', category=ParameterWarning)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf')))
ffxml_filename = get_fn('charmm.xml', written=True)
params.write(
ffxml_filename,
provenance=dict(
OriginalFiles='par_all36_prot.prm & top_all36_prot.rtf',
Reference='MacKerrel'),
charmm_imp=True)
forcefield = app.ForceField(ffxml_filename)
def test_write_xml_parameters_gaff(self):
""" Test writing XML parameters loaded from Amber GAFF parameter files """
leaprc = StringIO("""\
parm10 = loadamberparams gaff.dat
""")
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet.from_leaprc(leaprc))
citations = """\
Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and bond type perception in molecular mechanical calculations". Journal of Molecular Graphics and Modelling , 25, 2006, 247260.
Wang, J., Wolf, R. M.; Caldwell, J. W.;Kollman, P. A.; Case, D. A. "Development and testing of a general AMBER force field". Journal of Computational Chemistry, 25, 2004, 1157-1174.
"""
ffxml_filename = get_fn('gaff.xml', written=True)
params.write(ffxml_filename,
provenance=dict(OriginalFile='gaff.dat',
Reference=citations))
forcefield = app.ForceField(ffxml_filename)
def test_write_xml_parameters_antechamber(self):
""" Test writing XML residue definition from Antechamber mol2 """
leaprc = "molecule = loadmol2 %s\n" % get_fn('molecule.mol2')
leaprc += "loadamberparams %s\n" % get_fn('molecule.frcmod')
leaprc = StringIO(leaprc)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet.from_leaprc(leaprc),
remediate_residues=False)
ffxml_filename = get_fn('residue.xml', written=True)
params.write(ffxml_filename)
try:
forcefield = app.ForceField(ffxml_filename)
except KeyError:
# A KeyError is expected
pass
else:
assert False, "app.ForceField() should fail with a KeyError when residue templates without parameters are not removed, but it did not."
def test_ljforce_charmm(self):
""" Test writing LennardJonesForce without NBFIX from Charmm parameter files and reading them back into OpenMM ForceField """
charmm_params = pmd.charmm.CharmmParameterSet(
get_fn('par_all36_prot.prm'), get_fn('top_all36_prot.rtf'))
openmm_params = openmm.OpenMMParameterSet.from_parameterset(
charmm_params)
#openmm_params.write(get_fn('charmm.xml', written=True),
ffxml_filename = get_fn('charmm36.xml')
openmm_params.write(
ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm & top_all36_prot.rtf',
Reference='MacKerrell'),
separate_ljforce=True)
forcefield = app.ForceField(ffxml_filename)
def test_ljforce_charmm(self):
""" Test writing LennardJonesForce without NBFIX from Charmm parameter files and reading them back into OpenMM ForceField """
charmm_params = pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf'))
openmm_params = openmm.OpenMMParameterSet.from_parameterset(charmm_params)
#openmm_params.write(get_fn('charmm.xml', written=True),
ffxml_filename = get_fn('charmm36.xml')
openmm_params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm & top_all36_prot.rtf',
Reference='MacKerrell'
),
separate_ljforce=True
)
forcefield = app.ForceField(ffxml_filename)
# Parameterize alanine tripeptide in vacuum
pdbfile = app.PDBFile(get_fn('ala_ala_ala.pdb'))
system = forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
def test_write_xml_parameters_charmm(self):
""" Test writing XML parameter files from Charmm parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf'),
get_fn('toppar_water_ions.str')))
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm, top_all36_prot.rtf',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
# Parameterize alanine tripeptide in vacuum
pdbfile = app.PDBFile(get_fn('ala_ala_ala.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.NoCutoff)
# Parameterize ACE-NME in water
pdbfile = app.PDBFile(get_fn('2igd_924wat.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.PME)
def test_write_xml_parameters(self):
""" Test writing XML parameters loaded from Amber files """
leaprc = StringIO("""\
logFile leap.log
#
# ----- leaprc for loading the ff14SB force field
# ----- NOTE: this is designed for PDB format 3!
# Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "HZ" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OP" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CX" "C" "sp3" }
{ "C8" "C" "sp3" }
{ "2C" "C" "sp3" }
{ "3C" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "CS" "C" "sp2" }
{ "C" "C" "sp2" }
{ "CO" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "C5" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "Ca" "sp3" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "NY" "N" "sp2" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "EP" "" "sp3" }
{ "F" "F" "sp3" }
{ "Cl" "Cl" "sp3" }
{ "Br" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "F-" "F" "sp3" }
{ "Cl-" "Cl" "sp3" }
{ "Br-" "Br" "sp3" }
{ "I-" "I" "sp3" }
{ "Li+" "Li" "sp3" }
{ "Na+" "Na" "sp3" }
{ "K+" "K" "sp3" }
{ "Rb+" "Rb" "sp3" }
{ "Cs+" "Cs" "sp3" }
{ "Mg+" "Mg" "sp3" }
# glycam
{ "OG" "O" "sp3" }
{ "OL" "O" "sp3" }
{ "AC" "C" "sp3" }
{ "EC" "C" "sp3" }
}
#
# Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#
# Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
#
# Load water and ions
#
#loadOff atomic_ions.lib
#loadOff solvents.lib
#HOH = TP3
#WAT = TP3
#
# Define the PDB name map for the amino acids and nucleic acids
#
addPdbResMap {
{ 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "G" "G5" } { 1 "G" "G3" }
{ 0 "A" "A5" } { 1 "A" "A3" }
{ 0 "C" "C5" } { 1 "C" "C3" }
{ 0 "U" "U5" } { 1 "U" "U3" }
{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
# some old Amber residue names for RNA:
{ 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
{ 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
{ 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
{ 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
# some really old Amber residue names, assuming DNA:
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
# uncomment out the following if you have this old style RNA files:
# { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" }
# { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" }
# { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" }
# { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" }
}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "O2*" "O2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'" }
{ "H2*2" "H2''" }
{ "H2'1" "H2'" }
{ "H2'2" "H2''" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'" }
{ "H5*2" "H5''" }
{ "H5'1" "H5'" }
{ "H5'2" "H5''" }
{ "HO'2" "HO2'" }
{ "H5T" "HO5'" }
{ "H3T" "HO3'" }
{ "O1'" "O4'" }
{ "OA" "OP1" }
{ "OB" "OP2" }
{ "O1P" "OP1" }
{ "O2P" "OP2" }
}
#
# assume that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
""")
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet.from_leaprc(leaprc))
ffxml_filename = get_fn('amber_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(OriginalFile='leaprc.ff14SB',
Reference=[
'Maier and Simmerling',
'Simmerling and Maier'
],
Source=dict(Source='leaprc.ff14SB',
sourcePackage='AmberTools',
sourcePackageVersion='15')))
forcefield = app.ForceField(ffxml_filename)
# Make sure the forcefield can handle proteins with disulfide bonds
pdbfile = app.PDBFile(get_fn('3qyt_fix.pdb'))
forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
