Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd' for a system with a non-bonded cofactor

I'm using a pdb with a nonbonded cofact (181 residues for the protein and 10 for the cofactor). I've tried to use the commands from the tutorial but get the errors:

> pdb <- read.pdb("nacl_5k_zn_A75_C1/nowat.pdb")
> modes <- nma(pdb)
 Building Hessian...        Done in 0.149 seconds.
 Diagonalizing Hessian...   Done in 1.186 seconds.
Warning message:
In nma.pdb(pdb) :
  Possible multi-chain structure or missing in-structure residue(s) present
  Fluctuations at neighboring positions may be affected.
> cij <- dccm(modes)
  |======================================================================| 100%
> net <- cna(cij, cutoff.cij=0.3)
Warning messages:
1: In (function (graph, weights = E(graph)$weight, directed = TRUE,  :
  At community.c:460 :Membership vector will be selected based on the lowest modularity score.
2: In (function (graph, weights = E(graph)$weight, directed = TRUE,  :
  At community.c:467 :Modularity calculation with weighted edge betweenness community detection might not make sense -- modularity treats edge weights as similarities while edge betwenness treats them as distances
> plot(net, pdb, full = TRUE, vertex.label.cex=0.7)
Obtaining layout from PDB structure
Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd'

I don't know how to diagnose this problem. Inspecting cij found no NAs. Thanks for any help. my sys info is sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] igraph_1.2.2 bio3d_2.3-4

loaded via a namespace (and not attached): [1] magrittr_1.5 parallel_3.2.3 tools_3.2.3 Rcpp_1.0.0
[5] grid_3.2.3 pkgconfig_2.0.2 tcltk_3.2.3

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