ANM Application

Run the ClustENM(D) hybrid simulation method, combining clustering, ENM NMA and MD.

prody.apps.prody_apps.prody_clustenm.prody_clustenm(pdb, **kwargs)[source]

Run ClustENM(D) for pdb.

Parameters:

  • altloc – alternative location identifiers for residues used in the simulations, default is 'A'

  • cutoff – cutoff distance (A), default is '15.'

  • extend – write NMD file for the model extended to “backbone” (“bb”) or “all” atoms of the residue, model must have one node per residue, default is ''

  • figall – save all figures, default is False

  • figcc – save cross-correlations figure, default is False

  • figdpi – figure resolution (dpi), default is 300

  • figformat – figure file format, default is 'pdf'

  • figheight – figure height (inch), default is 6.0

  • figsf – save square-fluctuations figure, default is False

  • figwidth – figure width (inch), default is 8.0

  • fit_resolution – resolution for blurring structures for fitting cc, default is 5

  • fitmap – map to fit by filtering conformations like MDeNMD-EMFit, default is None

  • forcefield – Alternative force field pair tuple for protein then solvent from openmm, default is 'None'

  • gamma – spring constant, default is '1.'

  • ionicStrength – total concentration (M) of ions (positive and negative), excluding those to neutralize, default is 0.0

  • kdtree – use kdtree for Hessian, default is False

  • map_cutoff – min_cutoff for passing map for fitting, default is 0

  • maxIterations – maximum number of iterations of energy minimization, 0 means until convergence, default is 0

  • maxclust – maximum number of clusters for each generation, can be tuple of floats, default is 'None'

  • membrane – whether to include the explicit membrane model, default is False

  • model – index of model that will be used in the simulations, default is 1

  • multiple – whether each conformer will be saved as a separate PDB file, default is False

  • mzscore – modified z-score threshold to label conformers as outliers, default is 3.5

  • nconfs – number of new conformers from each one from previous generation, default is 50

  • ngens – number of generations, default is 5

  • nmodes – number of non-zero eigenvectors (modes) to calculate, default is 10

  • no_outlier – whether to not exclude outliers in each generation when using implicit solvent (always False for explicit), default is False

  • no_sim – whether a short MD simulation is not performed after energy minimization (otherwise it is), default is False

  • nproc – number of processors, default is 0

  • npzmatrices – write matrix to compressed ProDy data file, default is False

  • numdelim – number delimiter, default is ' '

  • numext – numeric file extension, default is '.txt'

  • numformat – number output format, default is '%12g'

  • outall – write all outputs, default is False

  • outcc – write cross-correlations, default is False

  • outcov – write covariance matrix, default is False

  • outdir – output directory, default is '.'

  • outeig – write eigenvalues/vectors, default is False

  • outhm – write cross-correlations heatmap file, default is False

  • outnpz – write compressed ProDy data file, default is False

  • outscipion – write continuousflex modes directory and sqlite, default is False

  • outsf – write square-fluctuations, default is False

  • padding – padding distance to use for solvation (nm), default is 1.0

  • parallel – whether conformer generation will be parallelized, default is False

  • platform – openmm platform (OpenCL, CUDA, CPU or None), default is None

  • prefix – output file prefix, default is '_clustenm'

  • replace_filtered – whether to keep sampling again to replace filtered conformers, default is False

  • rmsd – average RMSD of new conformers from previous ones, can be tuple of floats, default is '1.'

  • select – atom selection, default is 'all'

  • solvent – solvent model to be used, either imp for implicit or exp for explicit, default is 'imp'

  • sparse – use sparse matrices, default is False

  • t_steps_g – number of 2.0 fs MD time steps in each generation, can be tuple of floats, default is '7500'

  • t_steps_i – number of 2.0 fs MD time steps for initial structure, default is 1000

  • temp – temperature at which simulations are conducted, default is 303.15

  • threshold – RMSD threshold to apply when forming clusters, can be tuple of floats, default is 'None'

  • tolerance – energy tolerance to which the system should be minimized in kJ/mole, default is 10.0

  • turbo – use memory-intensive turbo option for modes, default is False

  • v1 – whether to use original sampling method with complete enumeration of ANM modes, default is False

  • write_params – whether to write parameters, default is False