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tmpchem / computational_chemistry

Files used in TMP Chem videos on computational chemistry
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encountered error #6

Open abuhaby opened 4 years ago

abuhaby commented 4 years ago

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

abuhaby commented 4 years ago

I had no problem with running scripts under geometric_analysis directory. The above issue I posted is under molecular_mechanics directory. Also, I am not very good in python. I tried to follow your youtube lectures plus the github resources.