ANM Application

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

prody_clustenm(pdb, **kwargs)

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 "protein and name CA or nucleic and name P C4' C2"
• 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