Protein-related items

gmx do_dssp, gmx rama, gmx wheel

To analyze structural changes of a protein, you can calculate the radius of gyration or the minimum residue distances over time (see sec. Radius of gyration and distances), or calculate the RMSD (sec. Root mean square deviations in structure).

You can also look at the changing of secondary structure elements during your run. For this, you can use the program gmx do_dssp, which is an interface for the commercial program DSSP  176. For further information, see the DSSP manual. A typical output plot of gmx do_dssp is given in Fig. 61.

Fig. 61 Analysis of the secondary structure elements of a peptide in time.

One other important analysis of proteins is the so-called Ramachandran plot. This is the projection of the structure on the two dihedral angles $\varphi$ and $\psi$ of the protein backbone, see Fig. 62:

Fig. 62 Definition of the dihedral angles $\varphi$ and $\psi$ of the protein backbone.

To evaluate this Ramachandran plot you can use the program gmx rama. A typical output is given in Fig. 63.

Fig. 63 Ramachandran plot of a small protein.

When studying $\alpha$-helices it is useful to have a helical wheel projection of your peptide, to see whether a peptide is amphipathic. This can be done using the gmx wheel program. Two examples are plotted in Fig. 64.

Fig. 64 Helical wheel projection of the N-terminal helix of HPr.