Dear All,
I am using cdk-1.2.3 version and trying to get forcefield parameters for some
molecules. When I use the forcefieldConfigurator calss with mmff94 or mm2
forcefield, I get wrong atom type names assignements. I have done this several
times for many molecules and I get to the same conclusion. I have atached here
the code (for one molcule) I am using that configures the forcefield, assigns
the atom type names and print the atom type names for each atom in the
molecule. I also attached the atom types obtained from the MMFF94 forcefield
(REAL MMFF94) from other source and I know that there are correct.
I don't know if I am doing someting wrong or the routine that assigns the atome
types is not correct.
here is the code:
sp = SmilesParser(DefaultChemObjectBuilder.getInstance())
mol =
sp.parseSmiles("CN1CC2=C(N=CN2C2=C(C1=O)C(Cl)=CC=C2)C1=NOC(=N1)[...@](C)(O)CO")
ffc = ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.assignAtomTyps(mol);
atoms = mol.atoms().iterator()
atom_ID = 1
while atoms.hasNext():
atom_i = atoms.next()
print atom_ID,"Symbol :",atom_i.getSymbol()," Atom Type
:",atom_i.getAtomTypeName()
atom_ID += 1
Mol code : CID10091748
Mol smile : CN1CC2=C(N=CN2C2=C(C1=O)C(Cl)=CC=C2)C1=NOC(=N1)[...@](C)(O)CO
MMFF94 REAL MMFF94
1 Symbol : C Atom Type : C C
2 Symbol : N Atom Type : N NC=O
3 Symbol : C Atom Type : C C
4 Symbol : C Atom Type : Car C5A
5 Symbol : C Atom Type : C5 C5B
6 Symbol : N Atom Type : N2OX N5B
7 Symbol : C Atom Type : C5 C5A
8 Symbol : N Atom Type : N2OX NPYL
9 Symbol : C Atom Type : Car Car
10 Symbol : C Atom Type : Car Car
11 Symbol : C Atom Type : C= C=
12 Symbol : O Atom Type : O= O=
13 Symbol : C Atom Type : Car Car
14 Symbol : Cl Atom Type : CL CL
15 Symbol : C Atom Type : Car Car
16 Symbol : C Atom Type : Car Car
17 Symbol : C Atom Type : Car Car
18 Symbol : C Atom Type : C5 C5B
19 Symbol : N Atom Type : N2OX N5A
20 Symbol : O Atom Type : Oar Oar
21 Symbol : C Atom Type : C5 C5A
22 Symbol : N Atom Type : N2OX N5B
23 Symbol : C Atom Type : C C
24 Symbol : C Atom Type : C C
25 Symbol : O Atom Type : O O
26 Symbol : C Atom Type : C C
27 Symbol : O Atom Type : O O
MM2
1 Symbol : C Atom Type : C
2 Symbol : N Atom Type : N
3 Symbol : C Atom Type : C
4 Symbol : C Atom Type : Csp2
5 Symbol : C Atom Type : Csp2
6 Symbol : N Atom Type : NPYL
7 Symbol : C Atom Type : Csp2
8 Symbol : N Atom Type : N
9 Symbol : C Atom Type : Csp2
10 Symbol : C Atom Type : Csp2
11 Symbol : C Atom Type : Csp2
12 Symbol : O Atom Type : O=
13 Symbol : C Atom Type : Csp2
14 Symbol : Cl Atom Type : CL
15 Symbol : C Atom Type : Csp2
16 Symbol : C Atom Type : Csp2
17 Symbol : C Atom Type : Csp2
18 Symbol : C Atom Type : Csp2
19 Symbol : N Atom Type : NPYL
20 Symbol : O Atom Type : Oar
21 Symbol : C Atom Type : Csp2
22 Symbol : N Atom Type : NPYL
23 Symbol : C Atom Type : C
24 Symbol : C Atom Type : C
25 Symbol : O Atom Type : O
26 Symbol : C Atom Type : C
27 Symbol : O Atom Type : O
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