psico.nma
Normal mode calculation using external apps or libraries.
2011-2012 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
Functions
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PDBMAT and DIAGRTB wrapper |
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Anisotropic Network Model (ANM) analysis with ProDy. |
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- psico.nma.normalmodes_pdbmat(selection, cutoff=10.0, force=1.0, mass='COOR', first=7, last=10, choose='LOWE', substruct='RESI', blocksize=4, exe='pdbmat', diag_exe='diagrtb', prefix='mode', states=7, factor=-1, clean=1, quiet=1, async_=-1, *, _self=..., **kwargs)[source]
PDBMAT and DIAGRTB wrapper
Runs “pdbmat” and “diagrtb” and generates perturbed models for modes “first” to “last”. WARNING: May run for a long time.
PDBMAT computes the mass-weighted second derivatives energy matrix, using Tirion’s model, that is, an elastic network model (ENM). In such models, close particles (atoms) are linked by springs.
http://ecole.modelisation.free.fr/modes.html
Notes
Only considers ATOM records, if your model contains MSE residues or ligands that you want to consider, prepare it like this: mse2met (all) # for MSE residues alter (hetatm), type=’ATOM’ # for any hetatm
Arguments
selection = string: atom selection
cutoff = float: interaction distance cutoff in angstroem {default: 10}
force = float: interaction force constant {default: 1.0}
mass = string: origin of mass values {default: COOR}
first = int: first mode to create perturbed model {default: 7}
last = int: last mode to create perturbed model {default: 10}
choose = string: eigenvalues chosen {default: LOWE}
substruct = string: type of substructuring {default: RESI}
blocksize = int: nb of residues per block {default: 4}
- psico.nma.normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1, prefix='prody', states=7, factor=-1, quiet=1, *, _self=...)[source]
Anisotropic Network Model (ANM) analysis with ProDy.
Based on: http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html