simc: Computed Elastic Network Models for Switched-Off-List of...
In BioPhysConnectoR: BioPhysConnectoR

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

For each entry in the contact list the contact will be broken and the resulting covariance matrix and new B factors will be computed in the elastic network model. Furthermore the Frobenius norms between the original and the new covariance matrix can be evaluated.

simc(pdb, mj1 = NULL, mj2 = NULL, mj.avg = FALSE, cl = NULL,
     alpha = 82, cuts = 169, path = getwd(), inv2file = FALSE,
     bfacs = TRUE, frob = TRUE, loc = NULL, norm = FALSE,
     file = NULL, cluster = NULL)

`pdb`	file name of the PDB
`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 matrices is used as value for the interaction of any two amino acids
`cl`	optional contact list to process
`alpha`	strength of the peptide bond
`cuts`	squared cutoff distance
`path`	path to the output files
`inv2file`	logical, if TRUE the inverse Hessian matrix is written to a file, otherwise it will not be stored
`bfacs`	logical, if TRUE, the B factors are written to a file, otherwise they will not be stored
`frob`	logical, if TRUE, the Frobenius norm is computed
`loc`	dimensions `i1, j1, i2, j2` for a matrix subset of which the frobenius norm should be computed
`norm`	logical, if TRUE the Frobenius norm is computed for the normalized matrices
`file`	personalized file name prefix
`cluster`	snow cluster object created with `makeCluster()`

If no contact list is given, the full contact list is extracted from the PDB-file. Each contact (except covalent contacts) in the list is broken and the corresponding covariance matrix and B factors are computed. Those can be written into files. A user-defined contact list can be specified as well. For the computation of the Frobenius norm, different regions can be specified in loc as matrix. Each row determines a region [i1:j1,i2:j2] to be used for the norm. The routine is parallelized for the list of contacts using parLapply() from the package snow. If cluster is left at its default value the computaion is carries out in serial.

No values are returned.

Franziska Hoffgaard, Philipp Weil

Hamacher and McCammon (2005) Journal of Chemical Theory and Computation 2, 873.
Hamacher (2008) Gene 422, 30–36.
Tierney, Rossini, Li (2009) Int J Parallel Proc 37, 78–90.

sim, sims

## Not run: 
cl<-matrix(c(3,1,4,1,5,1,9,1,10,1,11,1,24,1,66,1,67,1,68,1),ncol=2,byrow=TRUE)
out<-simc(system.file("1KZK.pdb", package = "BioPhysConnectoR"), cuts = 169, cl=cl)

## Cluster example
makeCluster(2)->clu
out<-simc(system.file("1KZK.pdb", package = "BioPhysConnectoR"), cuts = 169, cl=cl, 
                  cluster=clu)
stopCluster(clu)

## End(Not run)