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I am trying to run the walkthrough tutorial on Chignoline and got the following error at initial step to generate the psf file, can you tell me what I missed?
---------------------------------------------------------------------------
InvalidIndexError Traceback (most recent call last)
Input In [29], in <cell line: 6>()
3 PDB_file = 'data/chignolin_cln025.pdb'
4 PSF_file = 'data/chignolin_ca_top.psf'
----> 6 pdb2psf_CA(PDB_file, PSF_file, bonds = True, angles = False)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/torchmd_cg/utils/psfwriter.py:7, in pdb2psf_CA(pdb_name_in, psf_name_out, bonds, angles)
6 def pdb2psf_CA(pdb_name_in, psf_name_out, bonds=True, angles=True):
----> 7 mol = Molecule(pdb_name_in)
8 mol.filter("name CA")
10 n = mol.numAtoms
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/molecule.py:299, in Molecule.__init__(self, filename, name, **kwargs)
296 self.viewname = name
298 if filename is not None:
--> 299 self.read(filename, **kwargs)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/molecule.py:1147, in Molecule.read(self, filename, type, skip, frames, append, overwrite, keepaltloc, guess, guessNE, _logger, **kwargs)
1145 for rr in readers:
1146 try:
-> 1147 mol = rr(fname, frame=frame, topoloc=tmppdb, **kwargs)
1148 except FormatError:
1149 continue
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/readers.py:1100, in PDBread(filename, mode, frame, topoloc, validateElements, uniqueBonds)
1098 if "element" in parsedtopo:
1099 idx, newelem = pdbGuessElementByName(parsedtopo.element, parsedtopo.name)
-> 1100 parsedtopo.at[idx, "element"] = newelem
1102 for field in topodtypes:
1103 if (
1104 field in parsedtopo
1105 and topodtypes[field] == str
1106 and parsedtopo[field].dtype == object
1107 ):
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexing.py:2274, in _AtIndexer.__setitem__(self, key, value)
2271 self.obj.loc[key] = value
2272 return
-> 2274 return super().__setitem__(key, value)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexing.py:2229, in _ScalarAccessIndexer.__setitem__(self, key, value)
2226 if len(key) != self.ndim:
2227 raise ValueError("Not enough indexers for scalar access (setting)!")
-> 2229 self.obj._set_value(*key, value=value, takeable=self._takeable)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/frame.py:3869, in DataFrame._set_value(self, index, col, value, takeable)
3867 else:
3868 series = self._get_item_cache(col)
-> 3869 loc = self.index.get_loc(index)
3871 # setitem_inplace will do validation that may raise TypeError
3872 # or ValueError
3873 series._mgr.setitem_inplace(loc, value)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexes/range.py:388, in RangeIndex.get_loc(self, key, method, tolerance)
386 except ValueError as err:
387 raise KeyError(key) from err
--> 388 self._check_indexing_error(key)
389 raise KeyError(key)
390 return super().get_loc(key, method=method, tolerance=tolerance)
File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexes/base.py:5637, in Index._check_indexing_error(self, key)
5633 def _check_indexing_error(self, key):
5634 if not is_scalar(key):
5635 # if key is not a scalar, directly raise an error (the code below
5636 # would convert to numpy arrays and raise later any way) - GH29926
-> 5637 raise InvalidIndexError(key)
InvalidIndexError: []
The text was updated successfully, but these errors were encountered:
I am trying to run the walkthrough tutorial on Chignoline and got the following error at initial step to generate the psf file, can you tell me what I missed?
The text was updated successfully, but these errors were encountered: