> Any pointers to where to start fixing this? > > I'm happy to do some programming, but it seems the problems lie deeper > in the code than in forcefieldgaff.cpp. > >
Ive had a look at this - I think the problem is in the gaussian input parsing the primary issue is that the SMILES from gaussian is [CH]1N(C=CN1C)CC rather than [CH]=1N(C=CN1C)CC (taken from pubchem for the molecule) note same is true for mol format - the real molecule has 2 double bonds assigned in the ring - the output from gaussian parsing only 1 charge does not seem to matter with [CH]=1N(C=CN1C)CC it seems to assign ca/na to the 5 membered ring I have a dirty python script which I was using to play with parameterization as per the function in forcefieldgaff.cpp (it simply emulates what the typing function was doing in c++ in python) - it is a playing script but I can send it to you if you want - my analysis is from the output of this script not running anything else in openbabel I suspect the issue in the guassian parsing is the difficulty of assigning integral bond orders from a partial double bond geometry David ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
