This analysis will create a Ramachandran plot for your peptide system in any range of trajectory files you desire.

All scripts necessary can be found in the following path in DT2:

/lustre/tcline/rama-analysis

1. Copy the tcl script “phipsi.txt” to your directory with the trajectory files you want to analyze.
2. Open the script to see the arguments necessary [start] [end] [filename] [output file name]
3. You may need to adjust the lines including the .psf and the .dcd file names to your system
4. Load the module vmd on the command line by typing “module load vmd” (this is not done on your computer at home but on the resource you are using)
5. If this does not work, check what the vmd module is by typing “module avail” and then loading the appropriate vmd module
6. Once inside of the VMD application, load the tcl script by typing “source phipsi.txt”
7. Then type “phipsi [start] [end] [filename] [output file name]”
8. Once it completes, you can check with the example output to see if it matches the format; example output found at the path:

/lustre/tcline/rama-analysis/ex-output

1. Once you have gathered all the data files you want for the blocks of trajectory files desired, transfer all of these data files to your home computer that has Matlab
2. In Matlab you'll upload “ramaplot.m” and navigate the working directory to the path where all your data files are
3. You'll need to edit the ~file~ variable containing the names of all the data files
4. Likewise, change the name of the plot titles to match the order of your data files in the variable ~titlelist~
5. Example output of the plots is found in the example output folder listed above

1. This analysis used the Matlab script “ResidGroupAnalysis.m”
2. As with the standard analysis, you'll need to adjust the ~file~ and ~titlelist~ variables
3. You also need to adjust the number of residues in your peptide with the variable ~residues~
4. The article https://www.sciencedirect.com/science/article/pii/S1359027896000466 shows the effectiveness of using this group analysis compared to standard per residue Ramachandran plots
5. Example output data is also found in the directory listed above