The file used for RMSD analysis is complex_wb.psf according to the NAMD tutorial. The sample file is attached: 15-07-57.png but, my file is like this: 15-03-51.png. What causes this file error and how can I fix it? Thanks for interest.
You have a PSF EXT (extended version) and in the file you show, the text is wrapping around because the window isn't wide enough. Open the file with TextEdit or in a terminal (vim $yourfile.psf) and then make the window wider and then the formats will visually look similar.
My guess is this file should load fine for your analysis as is.
Thank you so much. I fixed it. But I stil can't do RMSD analysis. As I understand it, the problem is in the complex_wb.psf file. But I don't know how to fix it. After opening the VMD program, I load the complex_wb.psf file and then I load the .dcd formatted file. It gives an error like Unable to molecul and in the terminal like this: