[Open Babel] Maximum size of molecule for OBForceField

[Martin H. <ma...@bl...>]

Dear OB List
I'm new on the mailing list and looking forward to good discussions.

Currently, we're trying to optimize a single side which we mutated in a 
protein using the below OB code (python). However, apparently the 
routines run out of memory. We use a protonated version of the 1LBS.pdb 
file (the unprotonated one seems to work). I believe its the size of the 
system which is too large. Can this be?
What is the maximum atom number available the OBForceField methods?

Thanks for any hints.

  #!/usr/bin/env python

  # ******************************
  # OpenBabel local minimization
  # Credit: Kasper Thofte
  # ..............................

  # ******************************
  # Variables:
  num_grad_steps = 50
  file_name_ini = 'test_ini.pdb'
  file_name_opt = 'test_opt.pdb'
  # (its not prefectly clear what these identifiers refer to)
  movable = [653,661,662,656,663,662,657,665,664,658,660,659]
  forceField = 'MMFF94'
  informat, outformat = 'pdb', 'pdb'
  # ..............................


  # ******************************
  # Setup
  from openbabel import *
  conv = OBConversion()
  conv.SetInAndOutFormats(informat, outformat)
  mol = OBMol()
  conv.ReadFile(mol, file_name_ini)
  cnstr = OBFFConstraints()
  # ..............................


  # ******************************
  # Define constraints
  FF = OBForceField.FindForceField(forceField)
  FF.Setup(mol)
  for atom in OBMolAtomIter(mol):
      Anum = atom.GetIdx()
      if Anum not in movable:
          cnstr.AddAtomConstraint(Anum)
      print Anum
  # ..............................


  # ******************************
  # Optimization
  FF.SetConstraints(cnstr)
  FF.ConjugateGradients(num_grad_steps)
  FF.GetCoordinates(mol)
  for atom in OBMolAtomIter(mol):
      print atom.GetAtomicNum(), atom.GetX(), atom.GetY(), atom.GetZ()
  # ..............................


  # ******************************
  # Write optimized file
  conv.WriteFile(mol, file_name_opt)
  # ..............................