def read_amber_conversion(self):
qlib = QLib("amber")
qlib.read_amber_lib("data/ff-amber14/amber12_mod.lib")
qlib.read_amber_lib("data/ff-amber14/arn.lib")
qlib.read_prepin_impropers("data/ff-amber14/prep/amino12.in")
qlib.read_prepin_impropers("data/ff-amber14/arn.prepi")
# remove head from ACE and tail from NME
cons = qlib.residue_dict["ACE"].connections
cons = [con for con in cons if "head" not in con]
qlib.residue_dict["ACE"].connections = cons
cons = qlib.residue_dict["NME"].connections
cons = [con for con in cons if "tail" not in con]
qlib.residue_dict["NME"].connections = cons
assert qlib.get_string() in open("data/qamber14.lib").read()
# write the files
#
libfn = args.output_basename + ".lib"
prmfn = args.output_basename + ".prm"
prmchkfn = args.output_basename + ".prm.chk"
print "Writing the library file: {}".format(libfn)
backup = backup_file(libfn)
if backup:
print "# Backed up '{}' to '{}'".format(libfn, backup)
outstring = """# Generated with {}, version {}
# Date: {}
#
{}
""".format(os.path.basename(__file__), __version__,
time.ctime(), qlib.get_string())
open(libfn, "w").write(outstring)
print "Writing the parameter file: {}".format(prmfn)
backup = backup_file(prmfn)
if backup:
print "# Backed up '{}' to '{}'".format(prmfn, backup)
outstring = """# Generated with {}, version {}
# Date: {}
#
{}
""".format(os.path.basename(__file__), __version__,
time.ctime(), qprm.get_string())
open(prmfn, "w").write(outstring)
print "Writing the parameter check file: {}".format(prmchkfn)
def test_ff14sb_conversion():
# Amber14FF to Qamber14
#
# Convert Amber14 lib (+prepin for impropers) and parm+frcmod to Q lib/prm
# Load the structure 'all_amino_acids.pdb' and build the topology
# Check the total bonding energy contributions and number of bonding terms
# and compare the library and parameter set with official qamber14.
#
qal = QLib("amber")
qap = QPrm("amber", ignore_errors=True) # duplicates
qal.read_amber_lib("data/ff-amber14/amber12_mod.lib")
qal.read_amber_lib("data/ff-amber14/arn.lib")
qal.read_prepin_impropers("data/ff-amber14/prep/amino12.in")
qal.read_prepin_impropers("data/ff-amber14/arn.prepi")
qap.read_amber_parm("data/ff-amber14/parm/parm10.dat")
qap.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# add options to parameters
for line in """\
name Q-Amber14SB
type AMBER
vdw_rule arithmetic !vdW combination rule (geometric or arithmetic)
scale_14 0.8333 ! electrostatic 1-4 scaling factor
switch_atoms off
improper_potential periodic
improper_definition explicit\
""".splitlines():
lf = line.split()
qap.options[lf[0]] = " ".join(lf[1:])
# remove head from ACE and tail from NME
cons = qal.residue_dict["ACE"].connections
cons = [con for con in cons if "head" not in con]
qal.residue_dict["ACE"].connections = cons
cons = qal.residue_dict["NME"].connections
cons = [con for con in cons if "tail" not in con]
qal.residue_dict["NME"].connections = cons
qas1 = QStruct("data/all_amino_acids.pdb", "pdb", ignore_errors=True)
qat = QTopology(qal, qap, qas1)
q_tors = sum([len(list(tor.prm.get_prms())) for tor in qat.torsions])
assert len(qat.bonds) == 464
assert len(qat.angles) == 829
assert len(qat.torsions) == 1221
assert q_tors == 1950
assert len(qat.impropers) == 102
be = sum([bond.calc()[0] for bond in qat.bonds])
ae = sum([ang.calc()[0] for ang in qat.angles])
te = sum([tor.calc()[0] for tor in qat.torsions])
ie = sum([imp.calc()[0] for imp in qat.impropers])
assert is_close(be, 181.2572830)
assert is_close(ae, 212.8539304)
assert is_close(te, 417.2919960)
assert is_close(ie, 22.8171235)
# compare with official lib
qa14_lib = open("data/qamber14.lib", "r").read()
qa14_prm = open("data/qamber14.prm", "r").read()
assert qal.get_string() in qa14_lib
assert qap.get_string() in qa14_prm
def test_convert_oplsaa(self):
qlib = QLib("oplsaa")
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qlib.read_ffld("data/ace_ash_nma.ffld11", qstruct)
ql_str = qlib.get_string()
assert ql_str == open("data/ace_ash_nma.lib").read()
def test_read_write_lib(self):
qlib = QLib("amber")
qlib.read_lib("data/qamber14.lib")
qlib.residue_dict.pop("HOH") # different order
ql_str2 = qlib.get_string()
assert ql_str2 in open("data/qamber14.lib", "r").read()
# write the files
#
libfn = args.output_basename + ".lib"
prmfn = args.output_basename + ".prm"
prmchkfn = args.output_basename + ".prm.chk"
print("Writing the library file: {}".format(libfn))
backup = backup_file(libfn)
if backup:
print("# Backed up '{}' to '{}'".format(libfn, backup))
outstring = """# Generated with {}, version {}
# Date: {}
#
{}
""".format(os.path.basename(__file__), __version__, time.ctime(),
qlib.get_string())
open(libfn, "w").write(outstring)
# make a list of unique torsion prms
# (generics for same atypes are returned from .prm_full as
# separate _PrmTorsion objects)
torsion_prms = [x.prm_full for x in qtop.torsions]
torsion_prms_unique = {x.prm_id: x for x in torsion_prms}.values()
improper_prms = [x.prm_full for x in qtop.impropers]
improper_prms_unique = {x.prm_id: x for x in improper_prms}.values()
print("Writing the parameter file: {}".format(prmfn))
backup = backup_file(prmfn)
if backup:
print("# Backed up '{}' to '{}'".format(prmfn, backup))
outstring = """# Generated with {}, version {}
switch_atoms off
improper_potential periodic
improper_definition explicit""".splitlines():
lf = line.split()
qap.options[lf[0]] = " ".join(lf[1:])
# remove head from ACE and tail from NME
cons = qal.residue_dict["ACE"].connections
cons = [con for con in cons if "head" not in con]
qal.residue_dict["ACE"].connections = cons
cons = qal.residue_dict["NME"].connections
cons = [con for con in cons if "tail" not in con]
qal.residue_dict["NME"].connections = cons
open("qamber14_gen.lib", "w").write(qal.get_string())
open("qamber14_gen.prm", "w").write(qap.get_string())
print "# Topology with converted parameters (and mol2):"
qas1 = QStruct("../all_amino_acids.mol2", "mol2")
qat = QTopology(qal, qap, qas1)
q_tors = sum([len(list(tor.prm.get_prms())) for tor in qat.torsions])
print "Bonds: ", len(qat.bonds)
print "Angles: ", len(qat.angles)
print "Torsions: ", len(qat.torsions)
print "Q Torsions (diff parms): ", q_tors
print "Impropers: ", len(qat.impropers)
print "Bond energy: ", sum([bond.calc()[0] for bond in qat.bonds])
print "Angle energy: ", sum([ang.calc()[0] for ang in qat.angles])
print "Torsion energy: ", sum([tor.calc()[0] for tor in qat.torsions])
print "Improper energy: ", sum([imp.calc()[0] for imp in qat.impropers])