full-atom mktrj.nma()

[Former user]

Hi, is it possible to extrapolate the motion along a mode computed with nma on CA and write a full atom structure to a pdb file ? Regards, NB.

[Xinqiu Yao]

Hi,

It is possible, but I don't see the point to do that. Do you just want an alternative representation for the NMA mode or you really want to see how all heavy atoms move? If it is latter, an all-atom based NMA could be the solution.

[Lars Skjærven]

Take the vector corresponding to each CA atom and duplicate it corresponding to the number of atoms in the residue. See the m$modes attribute. e.g m$modes[7, atom2xyz(1)] represents atom 1 for mode 7.

sele = atom.select(pdb, "protein")
pdb = trim.pdb(pdb, sele)
m = nma(pdb)
natoms <- sum(pdb$calpha)
times <- table(pdb$atom$resno)

maa <- NULL
for ( i in 1:natoms ) {
   tmp <- m$modes[atom2xyz(i), 7]
   maa <- c(maa, rep(tmp, times[i]))
}

# code from mktrj()
mag = 10; step = 1.25;
xyz = as.vector(pdb$xyz)
nstep <- c(seq(step, to = mag, by = step))
zcoor <- cbind(1) %*% nstep
scor <- function(x, u, m) {
      return(x * u + m)
}
plus <- sapply(c(zcoor), scor, u = maa, m = xyz)
minus <- sapply(c(-zcoor), scor, u = maa, m = xyz)
coor <- t(cbind(xyz, plus, plus[, rev(1:ncol(plus))], xyz, 
        minus, minus[, rev(1:ncol(minus))]))

write.pdb(pdb=pdb, xyz = coor, file = "all-atom_m7.pdb")

[Lars Skjærven]

There is also an experimental version of all-atom NMA in the feature_aanma branch you might want to check out:

pdb <- read.pdb("1etl")
pdb <- trim.pdb(pdb, "noh")
pdb <- trim.pdb(pdb, "notwater")

m <- aanma(pdb, outmodes="noh")
trj <- mktrj(m)
write.pdb(pdb, xyz=trj)

[Wen Huang]

tmp <- m$modes[7, atom2xyz(i)] should be: tmp <- m$modes[atom2xyz(i), 7]

[Lars Skjærven]

Thanks for spotting this ! I've updated my code snippet above.