GROMACS version: 2026.0
GROMACS modification: No
Hello, gromacs (and chemistry) newbie here. I have a set of NMR pdb structures where I am labelling each residue with its secondary structure. I initially used gmx DSSP for this as it’s the most widely used algorithm, however when plotting phi and psi angles coloured by assignment (using only a-helix and b-strand), it is just completely random. MDAnalysis’s DSSP does not exhibit this behaviour and can distinguish almost perfectly between the structures on the ramachandran plot, as well as delta 2D (which uses chemical shifts instead of pdb). I am confident that the code is correct between algorithms as they all have very similar output.
As taken from the gmx dssp documentation:
Note that
gmx dsspcurrently is not capable of reproducing the secondary structure of proteins whose structure is determined by methods other than X-ray crystallography (structures in .pdb format with incorrect values in the CRYST1 line) due to the incorrect cell size in such structures.
I’ve looked at a few papers that the current version of gmx dssp is based on, but I think I am limited by my lack of knowledge of X-ray crystallography as my studies so far have been purely NMR-based. I’m aware that the algorithm was trained on crystal structures as per the DSSP 4 publication, but I’m confused as to why the CRYST1 values appear to have such a huge impact to render the output useless.
My question here is: how does the gmx dssp algorithm use the CRYST1 cell size in it’s SS determination, and why does the absence of correct CRYST1 values appear to completely mess up the calculation?