I am a first time user of openMM, trying to use the "small residue template generator", as described in section "3.6.3.1. Small molecule residue template generators" of the tutorial here: http://docs.openmm.org/latest/userguide ... generators
to be able to run simulations of an enzyme with a ThDP cofactor (https://en.wikipedia.org/wiki/Thiamine_pyrophosphate)
Unfortunately, this does not work:
Code: Select all
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 - 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.
Code: Select all
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
ThDP_creation.py:
Code: Select all
# 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)