Hi,
I'm trying to implement an algorithm to determine bond orders into the
GROMACS MD package, and looked at the open babel version. There seems to
be a problem in the implementation however. If I convert the structure
(from pdb or gaussian log file) of dimethyl-sulfoixde to sdf the bond
order for the S=O bond is 1, whereas it should be 2.
% babel -ipdb dmso.pdb -osdf dmso.sdf
If I instead convert the structure to an InChi code, open babel print a
warning message about the bond, and adds a Hydrogen instead and does not
produce the correct InChi. There is apparently a mechanism that verifies
that the sum of bond orders is even, but it is resolved in the wrong
way, by adding a H instead of realizing there is a double bond.
The sdf output is therefore inconsistent from the inchi output.
Is there any way I can prevent H being added?
dmso.pdb:
HETATM 1 C MOL 1 -1.366 -0.812 0.188 1.00 0.00
C
HETATM 2 H MOL 2 -1.337 -1.791 -0.288 1.00 0.00
H
HETATM 3 H MOL 3 -1.272 -0.893 1.269 1.00 0.00
H
HETATM 4 H MOL 4 -2.289 -0.299 -0.071 1.00 0.00
H
HETATM 5 S MOL 5 0.000 0.223 -0.448 1.00 0.00
S
HETATM 6 C MOL 6 1.366 -0.812 0.188 1.00 0.00
C
HETATM 7 H MOL 7 1.337 -1.791 -0.288 1.00 0.00
H
HETATM 8 H MOL 8 2.289 -0.299 -0.071 1.00 0.00
H
HETATM 9 H MOL 9 1.272 -0.893 1.269 1.00 0.00
H
HETATM 10 O MOL 10 0.000 1.483 0.375 1.00 0.00
O
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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