Dear users: I am unsing Confab to screen bioactive conformers in a serie of molecules bearing aromatic rings linked by rotatble bonds. I noticed that Confab does not detect the whole set of rotatable bonds I expected to be rotated.
The structure is shown below with the rotatable bond I expected to be detected: <http://forums.openbabel.org/file/n4659190/Ligando-2-AllRotatable.png> However, after running Confab, only 2 rotatable bonds were detected: <http://forums.openbabel.org/file/n4659190/Ligando-2-detected.png> After reading the Confab paper, I see that " The first step of the algorithm is the identification of rotatable bonds. These are defined as all acyclic single bonds where both atoms of the bond are connected to at least two non-hydrogen atoms, but neither atom of the bond is sp-hybridised." so I expected the whole set of rotatable bonds to be indentified. Also I performed a structure minimization using Obminimize to discard any problem with bond distances, but the outcome is the same. Any hint on what may be wrong? Thank you very much in advance for the help, best regards Alfredo -- View this message in context: http://forums.openbabel.org/Confab-rotatable-bond-detection-tp4659190.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
