Greetings, I am trying to optimize the geometry of some of the molecules from the current D3R challenge (hence the "IMPORTANT" tag in the title), but RDKit returns this error:
**** Invariant Violation bad direction in linearSearch Violation occurred on line 231 in file /home/thomas/Programs/rdkit/Code/Numerics/Optimizer/BFGSOpt.h Failed Expression: status >= 0 **** Traceback (most recent call last): File "/home2/thomas/Documents/ConsScorTK/bin/run_MD.py", line 254, in <module> minimize_molecules(monames2repeat) File "/home2/thomas/Documents/ConsScorTK/bin/run_MD.py", line 239, in minimize_molecules more = ff.Minimize(energyTol=1e-4, forceTol=1e-3) RuntimeError: Invariant Violation bad direction in linearSearch Violation occurred on line 231 in file Code/Numerics/Optimizer/BFGSOpt.h Failed Expression: status >= 0 RDKIT: 2017.03.1.dev1 BOOST: 1_61 Below is the part of my code that does minimization (assuming that "mol" object exists): ff = AllChem.UFFGetMoleculeForceField(mol, confId=0) ff.Initialize() more = ff.Minimize(energyTol=1e-4, forceTol=1e-3) The initial geometries are my docking poses. Do you think that this is the source of the problem? You can download the structures (also attached) from this link: https://www.dropbox.com/s/pp9srlkemweboaf/failed_compounds.sdf.gz?dl=0 thanks in advance Thomas -- ====================================================================== Dr Thomas Evangelidis Post-doctoral Researcher CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35/2S049, 62500 Brno, Czech Republic email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
failed_compounds.sdf
Description: StarMath document
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