ForceField ( 'amber99sbildn.xml', 'amber99_obc.xml' ) system = forcefield.
#PYTHON 2.7.9 UTILS PACKAGE CODE#
This is relatively "standard" OpenMM # code for setting up a system. to_openmm () # Lets use the amber99sb-ildn forcefield with implicit solvent # and a langevin integrator. Under normal circumstances # circumstances, you shouldn't have much need for _fn # (unless you're contributing tests to mdtraj!) import mdtraj.testing pdb = mdtraj. We happen to have one inlcuded in the mdtraj # package for testing named "native.pdb". # First, lets find a PDB for alanine dipeptide, the system we'll # be simulating.
close ( ) ImportError: dlopen(/Users/rmcgibbo/miniconda/envs/2.7.9/lib/python2.7/site-packages/simtk/openmm/_openmm.so, 2): Library not loaded: from: /Users/rmcgibbo/miniconda/envs/2.7.9/lib/python2.7/site-packages/simtk/openmm/_openmm.so load_module ( '_openmm', fp, pathname, description ) 37 finally : 38 fp. close ( ) 39 return _mod -> 40 _openmm = swig_import_helper ( ) 41 del swig_import_helper 42 else : /Users/rmcgibbo/miniconda/envs/2.7.9/lib/python2.7/site-packages/simtk/openmm/openmm.py in swig_import_helper () 34 if fp is not None : 35 try : -> 36 _mod = imp. openmm import version /Users/rmcgibbo/miniconda/envs/2.7.9/lib/python2.7/site-packages/simtk/openmm/openmm.py in () 38 fp. openmm import app /Users/rmcgibbo/miniconda/envs/2.7.9/lib/python2.7/site-packages/simtk/openmm/_init_.py in () 11 12 import os, os. in () 8 9 from simtk import unit -> 10 import simtk. ImportError Traceback (most recent call last) Command-line trajectory conversion: mdconvert.Memory-limited two pass clustering with scipy.cluster.Plotting a Ramachandran map with matplotlib.Principle components analysis (PCA) with scikit-learn.Out-of-core calculations with md.iterload().Baker-Hubbard Hydrogen Bond Identification.Get the Dependencies (Not Required with Conda).
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