On 2014-10-24 14:20, Mohammad Mehdi Ghahremanpour wrote: > 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. >
We will try to find the issue which I suspect is in mol.cpp using git bisect. > Cheers! > Mohammad > > > >> On Oct 23, 2014, at 1:59 AM, Geoffrey Hutchison >> <geoff.hutchi...@gmail.com <mailto: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 >> > _______________________________________________ >> > OpenBabel-Devel mailing list >> > OpenBabel-Devel@lists.sourceforge.net <javascript:;> >> > 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 >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> <mailto:OpenBabel-Devel@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
