Hi All,
I used obenergy command from two different version of openbabel on the same
molecule, but I got two different output. The atom type is different.
The molecule is 4-methyloxazole. I once used the developer version and once
openbabel-2.3.2. Please have a look at the results presented below. Actually,
the atom type of the openbabel-2.3.2 is correct, but the atom type of the
developer version is not correct.
I am using the developer version in my programs, I have to use that, please
help me understand why the developer version of openbabel has problem to match
cc and cd atom types.
OpenBabel-2.3.2
A T O M T Y P E S
IDX TYPE
1 nb
2 cd
3 cc
4 os
5 cc
6 c3
7 h5
8 h4
9 hc
10 hc
11 hc
C H A R G E S
IDX CHARGE
1 -0.611963
2 0.849504
3 -0.511506
4 -0.339859
5 -0.372202
6 -0.571980
7 0.553831
8 0.423136
9 0.190915
10 0.199209
11 0.190915
S E T T I N G U P C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
COULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS
SETTING UP ANGLE CALCULATIONS...
COULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nb-cd-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nb-cd-c3, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nb-cc-os, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS
SETTING UP TORSION CALCULATIONS...
COULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c3, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cd-nb-cc-os, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cd-nb-cc-h5, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cd-cc-os-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION h4-cc-os-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cc-os-cc-nb, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cc-os-cc-h5, USING DEFAULT PARAMETERS
SETTING UP IMPROPER TORSION CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...
E N E R G Y
TOTAL BOND STRETCHING ENERGY = 257.478 kJ/mol
TOTAL ANGLE BENDING ENERGY = 26.167 kJ/mol
TOTAL TORSIONAL ENERGY = 0.000 kJ/mol
TOTAL IMPROPER-TORSIONAL ENERGY = 0.000 kJ/mol
TOTAL VAN DER WAALS ENERGY = -0.991 kJ/mol
TOTAL ELECTROSTATIC ENERGY = -142.973 kJ/mol
TOTAL ENERGY = 139.681 kJ/mol
Developer version:
A T O M T Y P E S
IDX TYPE RING
1 nd AL
2 cc AL
3 cc AL
4 os AL
5 cc AL
6 c3 NO
7 h5 NO
8 h4 NO
9 hc NO
10 hc NO
11 hc NO
C H A R G E S
IDX CHARGE
1 -0.611963
2 0.849504
3 -0.511506
4 -0.339859
5 -0.372202
6 -0.571980
7 0.553831
8 0.423136
9 0.190915
10 0.199209
11 0.190915
S E T T I N G U P C A L C U L A T I O N S
SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
COULD NOT FIND PARAMETERS FOR TORSION cc-cc-os-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION h4-cc-os-cc, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cc-os-cc-nd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR TORSION cc-os-cc-h5, USING DEFAULT PARAMETERS
SETTING UP IMPROPER TORSION CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...
E N E R G Y
TOTAL BOND STRETCHING ENERGY = 23.490 kJ/mol
TOTAL ANGLE BENDING ENERGY = 40.709 kJ/mol
TOTAL TORSIONAL ENERGY = 0.000 kJ/mol
TOTAL IMPROPER-TORSIONAL ENERGY = 0.000 kJ/mol
TOTAL VAN DER WAALS ENERGY = -0.991 kJ/mol
TOTAL ELECTROSTATIC ENERGY = -142.973 kJ/mol
TOTAL ENERGY = -79.765 kJ/mol------------------------------------------------------------------------------
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