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+ | ---- | ||
+ | ====== Ramachandran Analysis ====== | ||
+ | |||
+ | |||
+ | 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: | ||
+ | |||
+ | / | ||
+ | |||
+ | === Gathering the phi-psi data === | ||
+ | |||
+ | - Copy the tcl script " | ||
+ | - Open the script to see the arguments necessary [start] [end] [filename] [output file name] | ||
+ | - You may need to adjust the lines including the .psf and the .dcd file names to your system | ||
+ | - Load the module vmd on the command line by typing " | ||
+ | - If this does not work, check what the vmd module is by typing " | ||
+ | - Once inside of the VMD application, | ||
+ | - Then type " | ||
+ | - Once it completes, you can check with the example output to see if it matches the format; example output found at the path: | ||
+ | / | ||
+ | |||
+ | === Matlab Analysis === | ||
+ | |||
+ | - 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 | ||
+ | - In Matlab you'll upload " | ||
+ | - You'll need to edit the ~file~ variable containing the names of all the data files | ||
+ | - Likewise, change the name of the plot titles to match the order of your data files in the variable ~titlelist~ | ||
+ | - Example output of the plots is found in the example output folder listed above | ||
+ | |||
+ | === Group of 4 residue analysis === | ||
+ | |||
+ | - This analysis used the Matlab script " | ||
+ | - As with the standard analysis, you'll need to adjust the ~file~ and ~titlelist~ variables | ||
+ | - You also need to adjust the number of residues in your peptide with the variable ~residues~ | ||
+ | - The article [[https:// | ||
+ | - Example output data is also found in the directory listed above |
map.1538576961.txt.gz · Last modified: 2018/10/03 10:29 by admin