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encountered error #6

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abuhaby opened this issue Feb 1, 2020 · 1 comment
Open

encountered error #6

abuhaby opened this issue Feb 1, 2020 · 1 comment

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@abuhaby
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abuhaby commented Feb 1, 2020

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
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abuhaby commented Feb 1, 2020

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.

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