Gmx do_dssp -f md_0_1.xtc -s md_0_1.tpr -o ss.xpm

User discussions
1

GROMACS version:2023.3
I get GROMACS this week and I have to do some command on a peptide of 8 amino acid
it is my first time using gromacs the command line have been given by the instructor but no enough details about the lines. so i’m learning from different website and connecting the knowledge.
I’m at the line: gmx do_dssp -f md_0_1.xtc -s md_0_1.tpr -o ss.xpm
which i did not find anywhere so i do not know what the job here .
now i got another lines with 14 group and it ask me which group i need to select i do not know which group. can someone help
Group 0 ( System) has 12164 elements
Group 1 ( Protein) has 113 elements
Group 2 ( Protein-H) has 54 elements
Group 3 ( C-alpha) has 8 elements
Group 4 ( Backbone) has 24 elements
Group 5 ( MainChain) has 33 elements
Group 6 ( MainChain+Cb) has 40 elements
Group 7 ( MainChain+H) has 43 elements
Group 8 ( SideChain) has 70 elements
Group 9 ( SideChain-H) has 21 elements
Group 10 ( Prot-Masses) has 113 elements
Group 11 ( non-Protein) has 12051 elements
Group 12 ( Water) has 12051 elements
Group 13 ( SOL) has 12051 elements
Group 14 ( non-Water) has 113 elements
Select a group:

2

DSSP is based on backbone hydrogen bonding, so you need group 7 (MainChain+H).

3

thank you
so i did i selected group 1 by mistake and the time is not changing now it has been about 1h nothing is changing and can not select another group! i may mess it up

Select a group: 1
Selected 1: ‘Protein’
There are 8 residues in your selected group
dssp cmd=‘/usr/bin/dssp -i ddDXKc4A 2>/dev/null’
Reading frame 0 time 0.000
Back Off! I just backed up ddDXKc4A to ./#ddDXKc4A.1#

dssp cmd=‘/usr/bin/dssp -i ddDXKc4A 2>/dev/null’
Reading frame 0 time 0.000
Back Off! I just backed up ddDXKc4A to ./#ddDXKc4A.1#

4

It’s a very slow and inefficient program. Check to see if intermediate files are being created with current time stamps. If they aren’t, kill the command and make the proper selection.

5

thank you