nma.pdbs() extension to include other ff terms

[Former user]

nma.pdbs() does not work with other force fields like nma.pdb. It will be good to have it work with other ff.

[Lars Skjærven]

It should work:

>  modes1 <- nma(pdbs, ff="calpha")
>  modes2 <- nma(pdbs, ff="anm")

no?

[Lars Skjærven]

A quick test to see if passing argument ff=anm to nma.pdbs()works:

ids <- c("1a70_A", "1czp_A", "1frd_A")
files <- get.pdb(ids, split = TRUE, path = tempdir())
pdbs <- pdbaln(files, outfile = tempfile())

# use nma.pdbs() to calculate modes
modes <- nma(pdbs, rm.gaps=FALSE, full=TRUE, ff="anm")

# use nma.pdb() to calcaulate modes
pdb <- pdbs2pdb(pdbs, 1)
m <- nma(pdb[[1]], ff="anm")

# check if eigenvalues are the same
identical(m$L, modes$full.nma[[1]]$L)
[1] TRUE