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: [email protected]
[email protected]
website: https://sites.google.com/site/thomasevangelidishomepage/
failed_compounds.sdf
Description: StarMath document
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