Description Usage Arguments Details Value Author(s) References See Also Examples

For a given list of PDB-files the respective covariance matrices and resulting B factors are computed.

1 2 |

`pdbs` |
list of PDB file names |

`mj1` |
matrix for the intrachain interaction strengths |

`mj2` |
matrix for the interchain interaction strengths |

`mj.avg` |
logical, if TRUE only the average value of the interaction matrix is used as value for the interaction of any two amino acids |

`alpha` |
strength of the peptide bond |

`cuts` |
squared distance cutoff |

`path` |
path to the output files |

`cluster` |
snow cluster object created with |

Each PDB file is extracted. All features necessary for the computation of the covariance matrix
in the elastic network model are computed. Both the covariance matrix and the B factors are computed and written to a file. The computation is parallelized using `parLapply()`

from the package snow. If `cluster`

is left at its default value the computation is carried out in serial.

No values are returned. The B factors and inverse Hessian matrices are written into files.

Franziska Hoffgaard, Philipp Weil

Hamacher and McCammon (2005) *Journal of Chemical Theory and Computation* 2, 873.

Tierney, Rossini, Li (2009) *Int J Parallel Proc* 37, 78–90.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## Not run:
#build a list of pdb-files
pdbs<-list(system.file("1KZK.pdb", package = "BioPhysConnectoR"),
system.file("1EBY.pdb", package = "BioPhysConnectoR"))
sim(pdbs, cuts = 169)
## Cluster example
clu<-makeCluster(2)
sim(pdbs, cuts = 169, cluster = clu)
stopCluster(clu)
## End(Not run)
``` |

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