It seems that the atom charges being generated when converting to mol2
format do not take into account the formal charge on the atoms.
$ echo 'CC(=O)Nc1ccc2[nH+]c(C)cc([O-])c2c1' | obabel -i smiles -o mol2
--gen2d
@<TRIPOS>MOLECULE
*****
16 17 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 2.5981 -1.5000 0.0000 C.3 1 UNL1 0.0968
2 C 2.5981 -0.5000 0.0000 C.2 1 UNL1 0.2461
3 O 3.4641 0.0000 0.0000 O.2 1 UNL1 -0.2730
4 N 1.7321 0.0000 0.0000 N.am 1 UNL1 -0.1792
5 C 0.8660 -0.5000 0.0000 C.ar 1 UNL1 0.0737
6 C 0.8660 -1.5000 0.0000 C.ar 1 UNL1 0.0229
7 C 0.0000 -2.0000 0.0000 C.ar 1 UNL1 0.0774
8 C -0.8660 -1.5000 0.0000 C.ar 1 UNL1 0.2951
9 N -1.7321 -2.0000 0.0000 N.ar 1 UNL1 0.0711
10 C -2.5981 -1.5000 0.0000 C.ar 1 UNL1 0.2734
11 C -3.4641 -2.0000 0.0000 C.3 1 UNL1 0.1151
12 C -2.5981 -0.5000 0.0000 C.ar 1 UNL1 0.0549
13 C -1.7321 -0.0000 0.0000 C.ar 1 UNL1 -0.0795
14 O -1.7321 1.0000 0.0000 O.co2 1 UNL1 -0.8726
15 C -0.8660 -0.5000 0.0000 C.ar 1 UNL1 0.0563
16 C -0.0000 -0.0000 0.0000 C.ar 1 UNL1 0.0215
@<TRIPOS>UNITY_ATOM_ATTR
9 1
charge 1
14 1
charge -1
@<TRIPOS>BOND
1 1 2 1
2 2 3 2
3 2 4 am
4 4 5 1
5 5 6 ar
6 6 7 ar
7 7 8 ar
8 8 9 ar
9 9 10 ar
10 10 11 1
11 10 12 ar
12 12 13 ar
13 13 14 1
14 13 15 ar
15 8 15 ar
16 15 16 ar
17 5 16 ar
1 molecule converted
Note the charge assigned to atom 9 (N+) which is 0.0711, whereas you would
expect it to be close to +1. Is there a way to address this?
Thanks
Tim
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