Is it possible to change the distance cutoff in construction of ENM?

[Former user]

Is it possible to set user-defined distance cutoff for any force field to select connected CA atoms in ENM?

[Lars Skjærven]

Jepp. Note that all ENMs implemented in bio3d does not use a cutoff. e.g. the default calpha force field has no cutoff argument, but the ANM does:

pdb <- read.pdb("1hel")
m1 <- nma(pdb, ff="calpha")
m2 <- nma(pdb, ff="anm", cutoff=15)
m3 <- nma(pdb, ff="anm", cutoff=7)

If you want calpha ff with cutoff, you can try to make your own pair force constant function:

myff <- function (r, cutoff = 10, ...) 
{   

   # first part is the default calpha force field
    a <- 128 * 10^4
    b <- 8.6 * 10^2
    c <- 2.39 * 10^3

    # force contstants by calpha ff
    k <- ifelse(r < 4, b * (r) - c, a * (r)^(-6))

    # assign zero values to pairs with distance > cutoff 
    inds <- r > cutoff
    k[inds] <- 0
    return(k)
}

m4 <- nma(pdb, pfc.fun=myff)

Hope this helps.