Hi Paolo, I'm forwarding this to the development list itself -- as a quick summary, 2.3.1 has a small regression to MMFF94 in Cu (and presumably Fe) compounds, where the formal charge is set by a SDF "M CHG" line (as attached).
You said this was due to some changes in mdlformat.cpp -- can you give me some revision numbers in SVN? I'm not comfortable reverting mdlformat until we know exactly what caused the regression. There is undoubtedly a cleaner way to solve the problem. I'll also add the CU1PW1 file to the MMFF94 test set to prevent future regressions. Thanks very much, -Geoff On Dec 5, 2011, at 4:47 PM, Paolo Tosco wrote: > Dear Geoff, > > looking at my previous e-mail I can't understand a single word myself :-) so > I'll try to be clearer here. > I have found a small MMFF94-related regression in OpenBabel 2.3.1, which was > not there in the SVN version that I normally use. > > if you issue > > $ obenergy -ff MMFF94 CU1PW1.sdf > > with openbabel 2.3.1 you get > > A T O M T Y P E S > > IDX TYPE > 1 70 > 2 31 > 3 31 > 4 98 > > F O R M A L C H A R G E S > > IDX CHARGE > 1 0.000000 > 2 0.000000 > 3 0.000000 > 4 2.000000 > > P A R T I A L C H A R G E S > > IDX CHARGE > 1 -0.860000 > 2 0.430000 > 3 0.430000 > 4 2.000000 > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE & STRETCH-BEND CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > SETTING UP ELECTROSTATIC CALCULATIONS... > > E N E R G Y > > TOTAL BOND STRETCHING ENERGY = 0.23164 kcal/mol > TOTAL ANGLE BENDING ENERGY = 0.45413 kcal/mol > TOTAL STRETCH BENDING ENERGY = -0.08423 kcal/mol > TOTAL TORSIONAL ENERGY = 0.00000 kcal/mol > TOTAL OUT-OF-PLANE BENDING ENERGY = 0.00000 kcal/mol > TOTAL VAN DER WAALS ENERGY = 6.94628 kcal/mol > TOTAL ELECTROSTATIC ENERGY = -61.07838 kcal/mol > > TOTAL ENERGY = -53.53057 kcal/mol > > > which is wrong. > Reverting some of the changes that were made to formats/mdlformat.cpp fixes > the issue. The attached patch patch_mdlformat.patch (apply with patch -p0 < > patch_mdlformat.patch in the openbabel root dir) will apply those reverts. > However, probably those patches have been made for some reason, so what fixes > my problem might break something else; maybe you have a better fix. > > mdlformat.cpp currently shipped with OB 2.3.1 triggers a problem in > forcefield.cpp, which results in the MMFF atom typing of CU1PW1.sdf to fail. > In fact, if you apply the patch patch_forcefield.patch (which just adds a > couple of debug printf to forcefield.cpp), you'll see that the original > mdlformat.cpp causes a problem when the instruction > > _mol = mol; > > between the two added printf's is executed. Afterwards, all atoms have zero > formal charge, both those in mol and those in _mol, which seems quite odd to > me, since as far as I can understand mol should be unchanged (but I'm not so > much a C++ guy). This triggers faulty atom typing on CU1PW1's Cu(I) ion, > which is based on the formal charge. > My limited C++ skills suggest to me that when mol is copied onto _mol > something bad happens. > > However, I hope I have given you enough information to find a better fix than > mine, or accept mine. > > I hope now things are clearer. Sorry for my previous e-mail, I was REALLY > tired and hungry :-P and longing to go to dinner! > > Best regards, > Paolo > > -- > ========================================================== > Paolo Tosco, Ph.D. Phone: +39 011 6707680 > Department of Drug Science Fax: +39 011 6707687 > and Technology Mob: +39 348 5537206 > Via Pietro Giuria, 9 > 10125 Torino, Italy > http://open3dalign.org > E-mail:paolo.to...@unito.it http://open3dqsar.org > ========================================================== > > > > <patches.tar.bz2> --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/
CU1PW1.sdf
Description: chemical/molfile
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