Analysis

Secondary structure

DSSP

You can generate a plot of the secondary structure per residue versus time using Gromacs. You first need to make sure that the program DSSP is either installed on your computer (just try to run the command dssp and check if it works) or download it from the DSSP website. Now you need to export a variable that contains the full path to your DSSP executable:

export DSSP=/full/path/to/dssp    for bash shell
sentenv DSSP /full/path/to/dssp  for csh shell

You can get the full path to dssp by running the command which dssp. This step is only necessary to enable Gromacs to find the dssp executable. Now execute these three commands in order:

gmx do_dssp -f md_protein.xtc -s md_protein.tpr -o ss.xpm

gmx xpm2ps -f ss.xpm -o ss.eps -bx 1 -by 30

ps2pdf -sPAPERSIZE=ledger ss.eps ss.pdf

For the calculation of the secondary structure the coordinates of the sidechains are not of relevance. However, choosing the "Backbone" group would not be sufficient as this group does not contain the carbonyl O atom, which is needed for the characterization of the secondary structure (due to the formation of backbone hydrogen bonds). Thus choose "Mainchain" (Group 5) instead.

To reduce the time needed for the calculation of the secondary structure and also to improve the appearence of the final plot, you might want to pass the -tu ns (setting the time unit to ns instead of ps) together with -dt 1 so that the secondary structure will be analyzed only every 1 ns (considering that on shorter times not much secondary structure changes occur).

If the ps2pdf tool should not be installed, google to find a way to directly open the ss.eps file. Otherwise, open the obtained file ss.pdf with a pdf reader of your choice. You should obtain a plot that shows how the secondary structure of [KIGAKI]3 evolving with time, similar to the figure above.

https://application.wiley-vch.de/HOME/bioinformatik/prot/Prot_1d/ueb/1dprotueb.htm, https://www.peptideweb.com/index.php/ramachandran-plot-as-a-tool-for-peptide-and-protein-structures-quality-determination


Ramachandran Plot


A Ramachandran plot is a plot of the torsional angles - Phi (Φ) and Psi (Ψ) - of the residues contained in a protein. In sequence order, Φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and Ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran et. al., plotting the Φ values on the x-axis and the Ψ values on the y-axis. The torsional angles of each residue in a protein define its conformation. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance.

gmx rama generates a Ramachandran plot showing Φ and Ψ for all residues and snapshots. Select Group 1 for "Protein".

gmx rama -f md_protein.xtc -s md_protein.tpr -o rama_protein.xvg