simtk.org

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python ThDP_creation.py 
Traceback (most recent call last):
  File "ThDP_creation.py", line 2, in <module>
    from openforcefield.topology import Molecule
ModuleNotFoundError: No module named 'openforcefield'

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conda install - conda-forge openforcefield
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - -
  - conda-forge
  - openforcefield

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

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conda search -f openf*

openff-evaluator               0.3.3    pyhd8ed1ab_0  conda-forge         
openff-evaluator               0.3.4    pyhd8ed1ab_0  conda-forge         
openff-forcefields             1.3.0    pyh44b312d_0  conda-forge         
openff-recharge                0.0.1    pyhd8ed1ab_0  conda-forge         
openff-toolkit                 0.9.0    pyh44b312d_0  conda-forge         
openff-toolkit                 0.9.0    pyhd8ed1ab_1  conda-forge         
openff-toolkit                 0.9.1    pyhd8ed1ab_1  conda-forge         
openff-toolkit-base            0.9.0    pyhd8ed1ab_1  conda-forge         
openff-toolkit-base            0.9.1    pyhd8ed1ab_1  conda-forge 

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# Create an openforcefield Molecule object for benzene from SMILES
from openforcefield.topology import Molecule
molecule = Molecule.from_smiles('Cc2ncc(C[n+]1csc(CCOP(=O)(O)OP(=O)(O)O)c1C)c(N)n2')
# Create the SMIRNOFF template generator with the most up to date Open Force Field Initiative force field
from openmmforcefields.generators import SMIRNOFFTemplateGenerator
smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
# Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
from simtk.openmm.app import ForceField
forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
# Register the SMIRNOFF template generator
forcefield.registerTemplateGenerator(smirnoff.generator)

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conda install -c conda-forge openmmforcefields

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python ThDP_creation.py 
Traceback (most recent call last):
  File "ThDP_creation.py", line 2, in <module>
    from openforcefield.topology import Molecule
ModuleNotFoundError: No module named 'openforcefield'

Code: Select all

conda install -c conda-forge openforcefield
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - openforcefield

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Code: Select all

from openforcefield.topology import Molecule

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from openforcefield.topology import Molecule

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from openff.toolkit.topology import Molecule

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python ThDP_creation.py 
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
Source amber/protein.ff14SB.xml.offxml could not be read. If this is a file, ensure that the path is correct.
If the file is present, ensure it is in a known SMIRNOFF encoding.
Valid formats are: ['XML']
Parsing failed with the following error:
not well-formed (invalid token): line 1, column 5

Traceback (most recent call last):
  File "/home/gug/anaconda3/lib/python3.8/site-packages/openmmforcefields/generators/template_generators.py", line 1005, in __init__
    self._smirnoff_forcefield = openff.toolkit.typing.engines.smirnoff.ForceField(filename)
  File "/home/gug/anaconda3/lib/python3.8/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 357, in __init__
    self.parse_sources(sources, allow_cosmetic_attributes=allow_cosmetic_attributes)
  File "/home/gug/anaconda3/lib/python3.8/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 901, in parse_sources
    smirnoff_data = self.parse_smirnoff_from_source(source)
  File "/home/gug/anaconda3/lib/python3.8/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1135, in parse_smirnoff_from_source
    raise IOError(msg)
OSError: Source amber/protein.ff14SB.xml.offxml could not be read. If this is a file, ensure that the path is correct.
If the file is present, ensure it is in a known SMIRNOFF encoding.
Valid formats are: ['XML']
Parsing failed with the following error:
not well-formed (invalid token): line 1, column 5


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "ThDP_creation.py", line 16, in <module>
    test = SMIRNOFFTemplateGenerator(molecules=D7K, forcefield='amber/protein.ff14SB.xml')
  File "/home/gug/anaconda3/lib/python3.8/site-packages/openmmforcefields/generators/template_generators.py", line 1008, in __init__
    raise ValueError(f"Can't find specified SMIRNOFF force field ({forcefield}) in install paths")
ValueError: Can't find specified SMIRNOFF force field (amber/protein.ff14SB.xml) in install paths

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# Create an openforcefield Molecule object for benzene from SMILES
from openff.toolkit.topology import Molecule
D7K = Molecule.from_smiles('Cc1nc(N)c(C[n+]2c(C)c(CCO[P@](O)(OP(O)(O)=O)=O)sc2)cn1')
# Create the SMIRNOFF template generator with the most up to date Open Force Field Initiative force field
from openmmforcefields.generators import SMIRNOFFTemplateGenerator
smirnoff = SMIRNOFFTemplateGenerator(molecules=D7K)
# Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
from simtk.openmm.app import ForceField
forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
# Register the SMIRNOFF template generator
forcefield.registerTemplateGenerator(smirnoff.generator)
# You can now parameterize an OpenMM Topology object that contains the specified molecule.
# forcefield will load the appropriate GAFF parameters when needed, and antechamber
# will be used to generate small molecule parameters on the fly.

test = SMIRNOFFTemplateGenerator(molecules=D7K, forcefield='amber/protein.ff14SB.xml')
test.add_molecules(D7K)

from simtk.openmm.app import PDBFile
pdbfile = PDBFile('MODEL_WITH_COFACTOR-processed.pdb')
system = forcefield.createSystem(pdbfile.topology)