UsageError Protein_ligand tool: WARNING:openff.toolkit.utils.toolkit_registry: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 WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. #41
Cordial greetings I have had the following error in the installation of the tool in google colab which does not allow me to run the calculations, attached capture
@title Install dependencies
@markdown It will take a few minutes, please, drink a coffee and wait. ;-)
original_stdout = sys.stdout # Save a reference to the original standard output
with open('prolif.sh', 'w') as f:
sys.stdout = f # Change the standard output to the file we created.
print(prolif1)
print(prolif2)
print(prolif3)
sys.stdout = original_stdout # Reset the standard output to its original value
sys.path.append('/usr/local/lib/python3.7/site-packages/')
from openmm import app, unit
from openmm.app import HBonds, NoCutoff, PDBFile
from openff.toolkit.topology import Molecule, Topology
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.utils import get_data_file_path
import parmed as pmd
from biopandas.pdb import PandasPdb
import openmm as mm
from openmm import
from openmm.app import
from openmm.unit import *
import os
import urllib.request
import numpy as np
import MDAnalysis as mda
import py3Dmol
import pytraj as pt
import platform
import scipy.cluster.hierarchy
from scipy.spatial.distance import squareform
import scipy.stats as stats
import matplotlib.pyplot as plt
import pandas as pd
from scipy.interpolate import griddata
import seaborn as sb
from statistics import mean, stdev
from pytraj import matrix
from matplotlib import colors
from IPython.display import set_matplotlib_formats
!wget https://raw.githubusercontent.com/openforcefield/openff-forcefields/master/openforcefields/offxml/openff_unconstrained-2.0.0.offxml 2>&1 1>/dev/null
WARNING:openff.toolkit.utils.toolkit_registry: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
WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
This is not an issue, it's just a warning. I've tried the notebook and everything is working fine.
Please, run the next cells and everything should work.
pablo-arantes
commented
1 year ago
Cordial greetings I have had the following error in the installation of the tool in google colab which does not allow me to run the calculations, attached capture
@title Install dependencies
@markdown It will take a few minutes, please, drink a coffee and wait. ;-)
%%capture import sys !pip -q install py3Dmol 2>&1 1>/dev/null !pip install --upgrade MDAnalysis 2>&1 1>/dev/null !pip install git+https://github.com/pablo-arantes/biopandas 2>&1 1>/dev/null !pip install rdkit-pypi !pip install Cython !git clone https://github.com/pablo-arantes/ProLIF.git prolif1 = "cd /content/ProLIF" prolif2 = "sed -i 's/mdanalysis.*/mdanalysis==2.0.0/' setup.cfg" prolif3 = "pip install ."
original_stdout = sys.stdout # Save a reference to the original standard output
with open('prolif.sh', 'w') as f: sys.stdout = f # Change the standard output to the file we created. print(prolif1) print(prolif2) print(prolif3) sys.stdout = original_stdout # Reset the standard output to its original value
!chmod 700 prolif.sh 2>&1 1>/dev/null !bash prolif.sh >/dev/null 2>&1
install conda
!wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh !bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null !rm -r Miniconda3-latest-Linux-x86_64.sh /content/ProLIF prolif.sh !conda install -y -q -c conda-forge openmm=7.6 python=3.7 pdbfixer 2>&1 1>/dev/null !conda install -c conda-forge ambertools --yes 2>&1 1>/dev/null !conda install -c ambermd pytraj --yes 2>&1 1>/dev/null !conda install -c conda-forge parmed --yes 2>&1 1>/dev/null !conda install -c conda-forge openff-toolkit --yes 2>&1 1>/dev/null !conda install -c bioconda pybel --yes !conda install -c openbabel openbabel --yes
load dependencies
sys.path.append('/usr/local/lib/python3.7/site-packages/') from openmm import app, unit from openmm.app import HBonds, NoCutoff, PDBFile from openff.toolkit.topology import Molecule, Topology from openff.toolkit.typing.engines.smirnoff import ForceField from openff.toolkit.utils import get_data_file_path import parmed as pmd from biopandas.pdb import PandasPdb import openmm as mm from openmm import from openmm.app import from openmm.unit import * import os import urllib.request
import numpy as np import MDAnalysis as mda import py3Dmol import pytraj as pt import platform import scipy.cluster.hierarchy from scipy.spatial.distance import squareform import scipy.stats as stats import matplotlib.pyplot as plt import pandas as pd from scipy.interpolate import griddata import seaborn as sb from statistics import mean, stdev from pytraj import matrix from matplotlib import colors from IPython.display import set_matplotlib_formats !wget https://raw.githubusercontent.com/openforcefield/openff-forcefields/master/openforcefields/offxml/openff_unconstrained-2.0.0.offxml 2>&1 1>/dev/null
WARNING:openff.toolkit.utils.toolkit_registry: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 WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.