Unable to read dcd file

[Atul]

trtfile <- "/home/atulsharma/Desktop/SOP simulation/kif1a_atp_0/dcd/kif1a_atp_1_prodrun.dcd"

trj <- read.dcd(trtfile) NATOM = 2011 NFRAME= 10000 ISTART= 10000 last = 100010000 nstep = 0 nfile = 0 NSAVE = 10000 NDEGF = 0 version 24 |====== | 10%Error in readBin(trj, "numeric", size = 4, n = (a/4), endian = head$end) : invalid 'n' argument

session info

sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

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

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

other attached packages: [1] bio3d_2.3-3

loaded via a namespace (and not attached): [1] parallel_3.2.3 tools_3.2.3 yaml_2.1.18 Rcpp_0.12.16
[5] grid_3.2.3

[Xinqiu Yao]

Hi,

Please check if the dcd file is damaged or contains any broken part. I tried to open it with VMD and got following warning:

Warning: DCD header claims 10000 frames, file size indicates there are actually 1001 frames

Although VMD can still load it, bio3d needs correct header information to read it properly.

[Atul]

Thanks, for pointing out the problem. I solved that and now its working. Thanks for your time and help.