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normal Python error in DNA tutorial

  • denner
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7 years 2 months ago - 7 years 2 months ago #7070 by denner
Python error in DNA tutorial was created by denner
I am trying to go through the DNA tutorial here , but I keep running into problems in the analysis.

In both commands "python cgHeliParm.py -f dna.xtc -s dna.gro -o dna" and "python persistence-length-calculator.py -s run.gro -f run.xtc -n run.ndx -oplot test -b 100000" I end up with the python error:
persistence-length $ python persistence-length-calculator.py -s run.gro -f run.xtc -n run.ndx -oplot test -b 100000
Loading...
Group 0 (SC1_beads) has 200 elements

Only 1 groups in index file. Reading them all.
Traceback (most recent call last):
  File "persistence-length-calculator.py", line 144, in <module>
    ndx_group, coords, oplot = initializeMDreader()
  File "persistence-length-calculator.py", line 74, in initializeMDreader
    tseries1 = md.timeseries(md.ndxgs[0])
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/persistence-length/mdreader.py", line 712, in timeseries
    indices = [grp.indices() for grp in tjcdx_atgrps]
TypeError: 'numpy.ndarray' object is not callable

I am using Python 2.7.6, numpy 1.12.0, and MDAnalysis 0.15.0. Since all the files in the persistence length part are part of the tutorial I am not sure where to start looking to fix this.

I know that this is not directly a Martini question, but I hope you can help anyway.
Last edit: 7 years 2 months ago by denner. Reason: Wording.

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7 years 2 months ago #7074 by ifaustino
Replied by ifaustino on topic Python error in DNA tutorial
Dear denner,

We have updated both scripts to the latest version of MDAnalysis. You should be able to download them from:
cgmartini.nl/index.php/tutorials-general...ial-martini-dna-gmx5

Let us know if these solve your issues.
Thanks.

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7 years 2 months ago #7075 by denner
Replied by denner on topic Python error in DNA tutorial
Thank you for replying. That sounds terrific.

When I access your link I get an error: "You are not authorised to view this resource."

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7 years 2 months ago #7076 by ifaustino
Replied by ifaustino on topic Python error in DNA tutorial
Hi denner.

Sorry for the mistake. This should work:
cgmartini.nl/index.php/tutorials-general...tutorial-martini-dna
Let me know if this time the link works and the scripts of course.

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7 years 2 months ago #7077 by denner
Replied by denner on topic Python error in DNA tutorial
Hi ifaustino.

Yes - the link is fine and so are the scripts (I quickly tested the one in the persistence length folder). (I do get a "DeprecationWarning" from mdreader and a "FutureWarning: elementwise comparison failed" from matplotlib. Not sure how important they are.)

Thank you very much for your help :-)

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7 years 2 months ago #7078 by ifaustino
Replied by ifaustino on topic Python error in DNA tutorial
Hi denner,

Great. No worries about those warnings. As you say, it is related to the MDAnalysis/mdreader module warning for the next version.

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7 years 2 months ago #7079 by denner
Replied by denner on topic Python error in DNA tutorial
That's what I thought.
Thanks again for the help (and for making/maintaining the tutorial).

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7 years 2 months ago #7082 by denner
Replied by denner on topic Python error in DNA tutorial
Hi again.

It turns out when I go through the tutorial again it breaks down at the cgHeliParm.py command. I use Gromacs 4.6.7 if that is relevant.

The error I get is:
$ python cgHeliParm.py -f dna.xtc -s dna.gro -o dna
Loading...
Residues: 24 Snapshots: 5000
Iterating through trajectory...
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
Process Process-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
Process Process-2:
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    self.run()
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.outqueue.put((num, f(*args)))
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
Process Process-4:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
Process Process-11:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
Process Process-7:
    self.run()
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
Process Process-3:
    return rdr._reader()
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
Traceback (most recent call last):
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
Process Process-8:
    ka,la = lsfit(mol.residues.resnames[res],res)
    self._target(*self._args, **self._kwargs)
  File "cgHeliParm.py", line 29, in lsfit
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
Traceback (most recent call last):
    "Error: {2}".format(self.filename, parser, err))
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.run()
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    self.outqueue.put((num, f(*args)))
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
  File "cgHeliParm.py", line 29, in lsfit
    ka,la = lsfit(mol.residues.resnames[res],res)
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
    return rdr._reader()
  File "cgHeliParm.py", line 29, in lsfit
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
    "Error: {2}".format(self.filename, parser, err))
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
    self.outqueue.put((num, f(*args)))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
Process Process-9:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
Process Process-6:
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
Traceback (most recent call last):
    self._target(*self._args, **self._kwargs)
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
Process Process-12:
Process Process-5:
Traceback (most recent call last):
Traceback (most recent call last):
    return rdr._reader()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    self.outqueue.put((num, f(*args)))
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    self.run()
    return rdr._reader()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    ka,la = lsfit(mol.residues.resnames[res],res)
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 29, in lsfit
    self._target(*self._args, **self._kwargs)
  File "cgHeliParm.py", line 203, in get_params
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
    self.run()
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    "Error: {2}".format(self.filename, parser, err))
    self._target(*self._args, **self._kwargs)
    ka,la = lsfit(mol.residues.resnames[res],res)
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
  File "cgHeliParm.py", line 29, in lsfit
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
    ka,la = lsfit(mol.residues.resnames[res],res)
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"
/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py:477: DeprecationWarning: In version 0.16.0, use `residue.atoms.names` instead.
  DeprecationWarning)
Process Process-10:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 203, in fcaller
    self.outqueue.put((num, f(*args)))
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 108, in _parallel_launcher
    return rdr._reader()
  File "/home/dennis/Desktop/dna-tutorial/DNA_analysis/mdreader.py", line 1019, in _reader
    result = self.p_fn(*self.p_args, **self.p_kwargs)
  File "cgHeliParm.py", line 203, in get_params
    ka,la = lsfit(mol.residues.resnames[res],res)
  File "cgHeliParm.py", line 29, in lsfit
    stnd = MDAnalysis.Universe(library_path + 'CG_C_std.pdb')
  File "/home/dennis/.local/lib/python2.7/site-packages/MDAnalysis/core/AtomGroup.py", line 4343, in __init__
    "Error: {2}".format(self.filename, parser, err))
IOError: Failed to load from the topology file /home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb with parser <class 'MDAnalysis.topology.PDBParser.PDBParser'>.
Error: [Errno 5] Cannot open file or stream in mode='rt'.: "'/home/ignacio/scripts/dna.analysis/cgHeliParm/data/CG_C_std.pdb'"

Should I change a path in the script? I hope you can help.

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7 years 2 months ago #7083 by ifaustino
Replied by ifaustino on topic Python error in DNA tutorial
Hi denner,

Yes, something I forgot to change. You only need to change the library path to where you actually have those files.

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7 years 2 months ago #7084 by denner
Replied by denner on topic Python error in DNA tutorial
Of course. I completely missed the "data" folder was there...

I changed it to "path-to-here/dna-tutorial/DNA_analysis/data/", and now it works.
Thanks again!

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