Error Loading DCD file

[Noah]

Hi all,

I am new user to Bio3d and am trying to do some contact network analysis. I having an issue loading in a dcd file into Bio3d. After using VMD to create the initial DCD file, I attempted to load my DCD file into Bio3d and I have attached the DCD file here. After reading out an initial summary

" NATOM = 5139 NFRAME= 1 ISTART= 0 last = 1 nstep = 1 nfile = 1 NSAVE = 1 NDEGF = 0 version 24 Reading (x100)"

I receive the error "Error in txtProgressBar(1, nframes, style = 3) : must have 'max' > 'min.'" Additionally a warning message appears stating "In dcd.header(trj, verbose) : Check DCD header data is correct, particulary natom."

I read the thread in issue #291 and was not able to solve the problem.

Thank you all for taking the time to help!

Best, Noah

[Xinqiu Yao]

Hi,

Thanks for spotting it. It is an error related to just the display of a progress bar. It should be overcome by setting verbose=FALSE.

The warning indicates that the header of the DCD file might no be in a proper format (missing a title for example). Double check if the number of atoms and first a few coordinates are correct. If so, you can safely ignore the warning.

[Xinqiu Yao]

set min=0 in txtProgressBar call in read.dcd() to fix the error when input DCD file has only one frame and verbose=TRUE.

[Noah]

Hi,

That ended up working, thank you very much!

Best, Noah