def Assign_OPLS(Molecule, ChelpG=True):
# Assign OPLS TYPES and CLASSES
print "Finding OPLS Types and Classes"
print "------------------------------"
print "Element Type Class"
print "______________________________"
Fullerene = False
for Atom_Obj in Molecule.Atom_List:
Fullerene = Atom.Find_OPLS_ID(Atom_Obj, Fullerene)
#print Atom_Obj.Atom_ID, Atom_Obj.Element, Atom_Obj.OPLS_Type, Atom_Obj.OPLS_Class
# Open up OPLS FILE
OPLS_Path = Configure.Template_Path + "oplsaa.prm.txt"
OPLS_FILE = open(OPLS_Path, 'r')
File_Lines = OPLS_FILE.readlines()
# Initialize Parameters Lists
OPLS_Bonds = []
OPLS_Angles = []
OPLS_Dihedrals = []
OPLS_Impropers = []
OPLS_VDW = []
OPLS_CHARGE = []
# Fill in parameter list
for Line in File_Lines:
Line = Line.split()
try:
if Line[0] == "bond":
OPLS_Bonds.append(Line)
if Line[0] == "angle":
OPLS_Angles.append(Line)
if Line[0] == "torsion":
OPLS_Dihedrals.append(Line)
if Line[0] == "imptors":
OPLS_Impropers.append(Line)
if Line[0] == "vdw":
OPLS_VDW.append(Line)
if Line[0] == "charge":
OPLS_CHARGE.append(Line)
except:
continue
print "------------------------------------"
print "Finding VDW parameters"
print "------------------------------------"
print "Element, OPLS TYPE, Sigma, Epsilon"
print "------------------------------------"
i = 0
for Atom_Obj in Molecule.Atom_List:
for VDW in OPLS_VDW:
if int(VDW[1]) == Atom_Obj.OPLS_Type:
i += 1
Atom_Obj.Sigma = float(VDW[2])
Atom_Obj.Epsilon = float(VDW[3])
#print Atom_Obj.Atom_ID, Atom_Obj.Element, Atom_Obj.OPLS_Type, Atom_Obj.Sigma, Atom_Obj.Epsilon
if i == len(Molecule.Atom_List):
print "All atom types present and accounted for :)"
else:
print "Missing OPLS Type: Edit Find_OPLS_ID function in Atom.py"
if ChelpG == False:
print "--------------------------------"
print "Finding partial charges"
print "--------------------------------"
for Atom_Obj in Molecule.Atom_List:
for CHARGE in OPLS_CHARGE:
if int(CHARGE[1]) == Atom_Obj.OPLS_Type:
print Atom_Obj.OPLS_Type
print "CHelpG:", Atom_Obj.Charge
print "OPLS:", float(CHARGE[2])
Atom_Obj.Charge = float(CHARGE[2])
print "Neutralizing Molecule"
Q = 0.0
Num_Atoms = 0.0
for Atom_Obj in Molecule.Atom_List:
if Atom_Obj.Charge != 0.0:
Q += Atom_Obj.Charge
Num_Atoms += 1.0
print "Total Charge on Molecule is", Q
print "N is", Num_Atoms
try:
dQ = Q / Num_Atoms
except:
dQ = 0.0
print "dQ =", dQ
for Atom_Obj in Molecule.Atom_List:
if Atom_Obj.Charge != 0.0:
if Atom_Obj.Charge < 0.0:
Atom_Obj.Charge -= dQ
print "Adjusting Charge +"
if Atom_Obj.Charge > 0.0:
Atom_Obj.Charge -= dQ
print "Adjusting Charge -"
Q = 0.0
Num_Atoms = 0.0
for Atom_Obj in Molecule.Atom_List:
if Atom_Obj.Charge != 0.0:
Q += Atom_Obj.Charge
Num_Atoms += 1.0
print "Total Charge on Molecule is", Q
print "------------------------------------"
print "Finding Bonds"
print "------------------------------------"
print "Bond #, Orca eq, OPLS eq"
i = 0
for Bond_Obj in Molecule.Bond_List:
Bonded_Atoms = sorted(
[Bond_Obj.Bond_Master.OPLS_Class, Bond_Obj.Bond_Slave.OPLS_Class])
for B_OPLS in OPLS_Bonds:
if int(B_OPLS[1]) == Bonded_Atoms[0] and int(
B_OPLS[2]) == Bonded_Atoms[1]:
i += 1
Bond_Obj.kb = float(B_OPLS[3])
if Molecule.UnConverged:
Bond_Obj.req = float(B_OPLS[4])
Bond_Obj.Bond_ID = i
print i, Bond_Obj.req, B_OPLS[4], Bond_Obj.kb
print "-------------------------------------"
if i == len(Molecule.Bond_List):
print "All bonds present and accounted for :)"
else:
print "MISSING BOND PARAMETER!!!!!"
for Bond_Obj in Molecule.Bond_List:
if Bond_Obj.kb == 0:
print Bond_Obj.Bond_Master.OPLS_Class, Bond_Obj.Bond_Slave.OPLS_Class
# Set arbitrary value for bond constant
Bond_Obj.Kb = 300.0
print "-------------------------------------"
print "Finding Angles"
print "-------------------------------------"
print "Angle #, Orca eq, OPLS eq"
i = 0
for Angle_Obj in Molecule.Angle_List:
Angle_Slaves = sorted([
Angle_Obj.Angle_Slave1.OPLS_Class,
Angle_Obj.Angle_Slave2.OPLS_Class
])
for A_OPLS in OPLS_Angles:
if int(
A_OPLS[2]
) == Angle_Obj.Angle_Master.OPLS_Class and Angle_Slaves[0] == int(
A_OPLS[1]) and Angle_Slaves[1] == int(A_OPLS[3]):
i += 1
Angle_Obj.ka = float(A_OPLS[4])
if Molecule.UnConverged:
Angle_Obj.Angle_Eq = float(A_OPLS[5])
Angle_Obj.Angle_ID = i
print i, Angle_Obj.Angle_Eq, Angle_Obj.ka, float(A_OPLS[5])
print "-------------------------------------"
if i == len(Molecule.Angle_List):
print " All angles present and accounted for :)"
else:
print "MISSING ANGLE PARAMETER!!!"
for Angle_Obj in Molecule.Angle_List:
if Angle_Obj.ka == 0:
print Angle_Obj.Angle_Master.OPLS_Class, Angle_Obj.Angle_Slave1.OPLS_Class, Angle_Obj.Angle_Slave2.OPLS_Class
Angle_Obj.ka = 35.0
print "-------------------------------------"
print "Finding Dihedrals"
print "-------------------------------------"
i = 0
for Dihedral_Obj in Molecule.Dihedral_List:
Dihedral_Masters = sorted([
Dihedral_Obj.Dihedral_Master1.OPLS_Class,
Dihedral_Obj.Dihedral_Master2.OPLS_Class
])
Dihedral_Slaves = sorted([
Dihedral_Obj.Dihedral_Slave1.OPLS_Class,
Dihedral_Obj.Dihedral_Slave2.OPLS_Class
])
#print Dihedral_Slaves[0], Dihedral_Masters, Dihedral_Slaves[1]
for D_OPLS in OPLS_Dihedrals:
M1 = int(D_OPLS[2])
M2 = int(D_OPLS[3])
S1 = int(D_OPLS[1])
S2 = int(D_OPLS[4])
if Dihedral_Masters[0] == M1 and Dihedral_Masters[
1] == M2 and Dihedral_Slaves[0] == S1 and Dihedral_Slaves[
1] == S2:
i = i + 1
Dihedral_Obj.Coeffs[0] = float(D_OPLS[5])
Dihedral_Obj.Coeffs[1] = float(D_OPLS[8])
Dihedral_Obj.Coeffs[2] = float(D_OPLS[11])
Dihedral_Obj.Dihedral_ID = i
if i == len(Molecule.Dihedral_List):
print "All dihedrals present and accounted for :)"
else:
print "MISSING DIHEDRAL PARAMETERS!!!"
print "i =", i
print "Num Dih=", len(Molecule.Dihedral_List)
Molecule.Missing_Dihedrals = len(Molecule.Dihedral_List) - i
for Dihedral_Obj in Molecule.Dihedral_List:
if Dihedral_Obj.Dihedral_ID == 0:
i += 1
Dihedral_Obj.Dihedral_ID = i
print Dihedral_Obj.Dihedral_Slave1.OPLS_Class, Dihedral_Obj.Dihedral_Master1.OPLS_Class, Dihedral_Obj.Dihedral_Master2.OPLS_Class, Dihedral_Obj.Dihedral_Slave2.OPLS_Class
print Dihedral_Obj.Dihedral_Slave1.Atom_ID, Dihedral_Obj.Dihedral_Master1.Atom_ID, Dihedral_Obj.Dihedral_Master2.Atom_ID, Dihedral_Obj.Dihedral_Slave2.Atom_ID
print "Finding Improper interactions (Aromatic Carbons OPLS_CLASS=48)"
i = 0
for Atom_Obj in Molecule.Atom_List:
if Atom_Obj.OPLS_Class == 48:
i += 1
Temp_Bond_List = sorted(Atom_Obj.Bond_List,
key=lambda x: x.Element)
Molecule.Improper_List.append(
Improper.Improper(Atom_Obj, Temp_Bond_List[0],
Temp_Bond_List[1], Temp_Bond_List[2], 5.0,
180.0, i))
print "Found ", i, "Improper interactions"
print "---------------------------------------"
print " Force Field Building is complete"
print "---------------------------------------"
return
