> Hi! I am trying to run obenergy on the TERRA Quadruplex (PDB Code 3IBK) and I > am having trouble getting MMFF94 force field to calculate the energy. I am > not sure what is causing this problem (I have only basic knowledge in > computational chemistry) and I was wondering if any of you can help me out. > > SETTING UP BOND CALCULATIONS... > USING EMPIRICAL RULE FOR BOND STRETCHING 1-2 (IDX)... > COULD NOT FIND PARAMETERS FOR BOND 58-522 (IDX)... > obenergy: could not setup force field.
This PDB file is very strange. It gives a CONECT record (i.e., a bond) between the K cation (atom 58) and an oxygen (atom 522). Not surprisingly, GAFF and MMFF94 flag this as an error. I don't know the best solution, but I would look around to see if someone has defined a "real" topology for this PDB file, or I'd open it in a program like PyMol or Avogadro and remove all bonds to the K atoms and save the result as a Mol2 or CML file which better defines the accurate bonding in this system. In this case, I think it's clear that Open Babel is doing essentially The Right Thing and flagging an error before you get erroneous results. Hope that helps, -Geoff ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
