[OpenBabel-Devel] openbabel obenergy error with atomtype

Mohammad Ghahremanpour Thu, 02 Oct 2014 03:31:46 -0700

Hi

I executed this command obenergy -ff GAFF on 110-dichlorodecane molecule.
As you can see in the output below, for three hydrogens openbabel used X
instead of "hc". I checked my input file, and according to the coordinates,
the distance between these hydrogens and the carbon atom to which they are
connected is 1.09 that is in the range of C-H single bond. So why openbabel
could recognize them.


Thanks in advance for your help

Mohammad


A T O M   T Y P E S

IDX    TYPE    RING
1    c3    NO
2    c3    NO
3    c3    NO
4    c3    NO
5    c3    NO
6    c3    NO
7    cl    NO
8    c3    NO
9    c3    NO
10    c3    NO
11    c3    NO
12    cl    NO
13    X    NO
14    hc    NO
15    hc    NO
16    hc    NO
17    hc    NO
18    X    NO
19    hc    NO
20    hc    NO
21    hc    NO
22    X    NO
23    h1    NO
24    h1    NO
25    hc    NO
26    hc    NO
27    hc    NO
28    hc    NO
29    hc    NO
30    hc    NO
31    h1    NO
32    h1    NO

C H A R G E S

IDX    CHARGE
1    -0.176820
2    -0.176591
3    -0.180061
4    -0.173824
5    -0.191447
6    -0.195895
7    -0.170084
8    -0.176291
9    -0.191886
10    -0.174599
11    -0.198193
12    -0.166565
13    0.090902
14    0.089416
15    0.090412
16    0.093978
17    0.088220
18    0.092795
19    0.088065
20    0.121710
21    0.100407
22    0.117516
23    0.151664
24    0.146005
25    0.093261
26    0.094476
27    0.093655
28    0.094326
29    0.115455
30    0.115921
31    0.146857
32    0.147217

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...
SETTING UP IMPROPER TORSION CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
COULD NOT FIND VDW PARAMETERS FOR ATOM X, USING HYDROGEN VDW PARAMETERS
SETTING UP ELECTROSTATIC CALCULATIONS...

E N E R G Y

     TOTAL BOND STRETCHING ENERGY =    3.195 kJ/mol
     TOTAL ANGLE BENDING ENERGY =    7.950 kJ/mol
     TOTAL TORSIONAL ENERGY =    0.509 kJ/mol
     TOTAL IMPROPER-TORSIONAL ENERGY =    0.000 kJ/mol
     TOTAL VAN DER WAALS ENERGY = 441804.365 kJ/mol
     TOTAL ELECTROSTATIC ENERGY =  -67.730 kJ/mol

TOTAL ENERGY = 441748.288 kJ/mol

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[OpenBabel-Devel] openbabel obenergy error with atomtype

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