Error in cij.network[cij.network > 0]

[debra ragland]

Greetings,

I am trying to compute "net" via cna(cij) as shown in the vignettes on the site (very helpful tutorials by the way!) using my school's computing cluster. I want to compute for both protein (CA) and all ligand atoms for 1500 frames. For this I have done the following;

dcd <- read.dcd("CA_DRV.dcd")
pdb <- read.pdb("CA_DRV.pdb")
inds <- atom.select(pdb, resno = c(24:27, 85:90), elety = "CA", resid = "017", operator = "AND") #here I am trying to use both protein CA and all ligand ("017") atoms
trj <- fit.xyz(fixed = pdb$xyz, mobile = dcd,fixed.inds = inds$xyz, mobile.inds = inds$xyz)
cij <- dccm(trj)
net <- cna(cij)

However, I get the following error;

Error in cij.network[cij.network > 0] <- exp(-cij.network[cij.network >  : 
  NAs are not allowed in subscripted assignments

I have never encountered this error before, as I've not attempted to include the ligand in my calculations, does my problem lie in the way that I have tried to incorporate the ligand in "atom.select()"?

[Xinqiu Yao]

Hi,

When you combine 'CA' and ligand, you should use operator='OR' instead of 'AND' in the atom select.