Hi Geoff, If you remember my previous emails, the developer version often makes mistake in assigning SP2-conjugated double bonds in the ring systems. SP2-conjugated double bond should be cc-cd, but the developer version sometimes assigns cc-cc that is incorrect.
I compared the mol.cpp file between the developer master version and V-2-3-2 version. They are different, particularly in void OBMol::PerceiveBondOrders(). I compared these two files for this method and saw that the sections of Pass5 and Pass6 are different. Pass 5 checks for aromatic rings and assigns bonds, and Pass 6 assings remaining bond types ordered by electronegativity. Pass 6 also recognizes possible SP2-hybrid atoms. That would be great if you could have look at the void OBMol::PerceiveBondOrders(). It may be useful to debug this problem. Cheers! Mohammad > On Oct 23, 2014, at 1:59 AM, Geoffrey Hutchison <geoff.hutchi...@gmail.com> > wrote: > > Atom typing for force fields is not done through the internal type > translation. For fidelity, it is done by the force field code itself. > > I haven't had time to look at code changes, but I suspect there have been > GAFF patches since 2.3.2. > > Geoff > > On Wednesday, October 22, 2014, David van der Spoel <sp...@xray.bmc.uu.se > <mailto:sp...@xray.bmc.uu.se>> wrote: > > > On 22 okt 2014, at 15:21, Geoffrey Hutchison <geoff.hutchi...@gmail.com > <javascript:;>> wrote: > > >> I am using the developer version in my programs, I have to use that, > >> please help me understand why the developer version of openbabel has > >> problem to match cc and cd atom types. > > > > The difference is that I noticed v2.3.2 was still using the Ghemical force > > field as the default, which isn't a good thing. You definitely want atom > > typing and energies from MMFF94, which is what's used in the developer > > "master" version. > > > > Hope that helps, > > We are using Gaff. But openbabel uses an internal type first, right? > > -Geoff > > > > > > ------------------------------------------------------------------------------ > > Comprehensive Server Monitoring with Site24x7. > > Monitor 10 servers for $9/Month. > > Get alerted through email, SMS, voice calls or mobile push notifications. > > Take corrective actions from your mobile device. > > http://p.sf.net/sfu/Zoho <http://p.sf.net/sfu/Zoho> > > _______________________________________________ > > OpenBabel-Devel mailing list > > OpenBabel-Devel@lists.sourceforge.net <javascript:;> > > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > <https://lists.sourceforge.net/lists/listinfo/openbabel-devel> > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net <javascript:;> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > <https://lists.sourceforge.net/lists/listinfo/openbabel-devel> > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel
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