DSSP on gromacs 2023

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Dear gromacs users

I have problems working “gmx dssp”. As you know, the command “gmx do_dssp” has been replaced by “gmx dssp” in gromacs 2023.

1- It seems that “-hmode gromacs” dont work and you have to use “-hmode dssp” instead. Is it normal or a bug?

2- The program produces only one output (with dat extension). It contains simply just the secondary structure of the structure in all simulation steps (without any data about axes or other data). How can I produce secondary structure count along simulation time in *.xvg format?

3- The secondary structure has been reported in dat file format with 9 characters, among them I don’t know the character “~” and “P” belong to what kind of secondary structure?

Thanks for your responses and comments.

2

  1. What do you mean “don’t work”? I need some examples. Do your structure contains hydrogen atoms at all? -hmode gromacs sets program to use hydrogen atoms directly from the structure, while -hmode dssp creates hydrogen peudo-atoms for each residue. If your structure lacks hydrogens there’s definitely would be a problem using -hmode gromacs option.

  2. That’s the neat part, you don’t. Maybe I’ll add this feature someday, but for now I don’t consider it to be necessary.

  3. “~” means “loop” (aka “no secondary structure”) and “P” means “Polyproline helix”.

3

Dear sorcerer
thank you for your response
about your response to question 2, a) I want to show the secondary structure during simulation time graphically. How can I do this from just a *.dat file? As I see, in this *.dat file the data is very raw, without any axis. b) What are the applications of flags “-xvg” and “-tu”?

4

For now, to make any kind of graph, you will need to write a script for yourself. The “-xvg” and “-tu” options do not work. However, I plan to add plotting along with a mod to analyze hydrogen bonds using a geometric method.

What do you think, what should be the graphical representation of the output data? Graph of the number of secondary structures in all frames? Many graphs of secondary structures per each frame? A map of secondary structures for the whole structure? (This is one of the reasons why we haven’t added a graphical display of data yet.)