Protein-related items¶
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.
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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
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Fig. 62 Definition of the dihedral angles
To evaluate this Ramachandran plot you can use the program gmx rama. A typical output is given in Fig. 63.
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Fig. 63 Ramachandran plot of a small protein.¶
When studying
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Fig. 64 Helical wheel projection of the N-terminal helix of HPr.¶