Please, can you help me with the following problem?: I have this PDB file (sugar from Protein Data Bank): HETATM 3781 C1 MAN C1129 35.524 5.379 57.298 1.00 26.66 C HETATM 3782 C2 MAN C1129 34.930 6.750 56.924 1.00 26.33 C HETATM 3783 C3 MAN C1129 33.464 6.454 56.622 1.00 26.11 C HETATM 3784 C4 MAN C1129 33.300 5.264 55.639 1.00 27.32 C HETATM 3785 C5 MAN C1129 34.075 4.044 56.187 1.00 26.81 C HETATM 3786 C6 MAN C1129 33.940 2.770 55.387 1.00 29.05 C HETATM 3787 O1 MAN C1129 35.436 5.171 58.706 1.00 28.59 O HETATM 3788 O2 MAN C1129 35.526 7.320 55.789 1.00 25.38 O HETATM 3789 O3 MAN C1129 32.846 7.632 56.180 1.00 27.40 O HETATM 3790 O4 MAN C1129 31.911 5.020 55.451 1.00 27.90 O HETATM 3791 O5 MAN C1129 35.457 4.383 56.289 1.00 22.18 O HETATM 3792 O6 MAN C1129 34.428 2.960 54.081 1.00 30.05 O --- In this file, the atoms C1 and O1 have a distance 1.426 A. Therefore the single bond is between them. Note: This C-O bond is the longest C-O bond in this molecule.
But when I convert this file to MOL, OpenBabel reports a double bond between C1 and O1. All other C-O bonds in the molecule are reported as single. And OpenBabel insists on the double bond even when I just add hydrogens to the PDB file. I used OpenBabel 2.3.2. Note: I do the conversion from PDB to MOL, because I need chirality data. And when the double bond is found, the chirality is not reported. Please, do you have some idea, where is a problem? Thank you very much for help. -- View this message in context: http://forums.openbabel.org/Error-in-double-bond-detection-tp4656494.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss