when i run below line in jupyter notebook
run ./scripts/molecular_mechanics/mm.py ./geom/prm/co.prm
i get the following errors
ValueError Traceback (most recent call last)
~\computational_chemistry-master\scripts\molecular_mechanics\mm.py in
24
25 # Read in molecular geometry and topology.
---> 26 molecule = molecule.Molecule(input_file_name)
27
28 # Calculate potential energy.
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\molecule.py in init(self, infile_name)
480 self.GetTopology()
481 elif (self.filetype == 'prm'):
--> 482 self.ReadInPrm()
483 self.UpdateInternals()
484
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\molecule.py in ReadInPrm(self)
504 input_rows = fileio.GetFileStringArray(self.infile)
505
--> 506 self.atoms = fileio.GetAtomsFromPrm(input_rows)
507 self.bonds = fileio.GetBondsFromPrm(input_rows)
508 self.angles = fileio.GetAnglesFromPrm(input_rows)
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\fileio.py in GetAtomsFromPrm(rows)
401 for row in rows:
402 if row and row[0].upper() == 'ATOM':
--> 403 atoms.append(GetAtomFromPrm(row))
404 return atoms
405
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\fileio.py in GetAtomFromPrm(row)
231 if not _IsType(float, ro) or not float(ro) > 0.0:
232 raise ValueError(
--> 233 'Atomic vdw radius must be positive numeric value: %s' % ro)
234 if not _IsType(float, eps) or not float(eps) >= 0.0:
235 raise ValueError(
ValueError: Atomic vdw radius must be positive numeric value: 0.0
when i run below line in jupyter notebook
run ./scripts/molecular_mechanics/mm.py ./geom/prm/co.prm
i get the following errors
ValueError Traceback (most recent call last)
~\computational_chemistry-master\scripts\molecular_mechanics\mm.py in
24
25 # Read in molecular geometry and topology.
---> 26 molecule = molecule.Molecule(input_file_name)
27
28 # Calculate potential energy.
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\molecule.py in init(self, infile_name)
480 self.GetTopology()
481 elif (self.filetype == 'prm'):
--> 482 self.ReadInPrm()
483 self.UpdateInternals()
484
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\molecule.py in ReadInPrm(self)
504 input_rows = fileio.GetFileStringArray(self.infile)
505
--> 506 self.atoms = fileio.GetAtomsFromPrm(input_rows)
507 self.bonds = fileio.GetBondsFromPrm(input_rows)
508 self.angles = fileio.GetAnglesFromPrm(input_rows)
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\fileio.py in GetAtomsFromPrm(rows)
401 for row in rows:
402 if row and row[0].upper() == 'ATOM':
--> 403 atoms.append(GetAtomFromPrm(row))
404 return atoms
405
~\computational_chemistry-master\scripts\molecular_mechanics\mmlib\fileio.py in GetAtomFromPrm(row)
231 if not _IsType(float, ro) or not float(ro) > 0.0:
232 raise ValueError(
--> 233 'Atomic vdw radius must be positive numeric value: %s' % ro)
234 if not _IsType(float, eps) or not float(eps) >= 0.0:
235 raise ValueError(
ValueError: Atomic vdw radius must be positive numeric value: 0.0