Explaination in dPCA

User discussions
1

Hi,
I am using the local version of Gromacs and I am following the steps from the article “Information-Driven, Ensemble Flexible Peptide Docking
Using HADDOCK”
At first, I did MD simulation and then dihedral PCA as mentioned in the article (to use some of the structures as starting points for docking).
There are 2 steps here I did not understand:

  1. gmx angle -f protein_bb.xtc -n dangle.ndx -or dangle.trr -type dihedral. This command returns “There are 12 dihedrals. Will fill 8 atom positions with cos/si”. Why will in not return 12? why did it choose only 8 of them?

  2. In specific cases (usually not the case) such as when running the peptides of 7pll (seq TAFQEPPPKPSRPKYRPPP) the file ““bindex-1_2.ndx” has many bins but in “shamlog-1_2.log” they don’t all appear, why?
    this is the output
    Minimum 0 at index 82 energy 11.366
    Minimum 1 at index 90 energy 0.000
    Minimum 2 at index 198 energy 0.324
    Minimum 3 at index 224 energy 11.366
    Minimum 4 at index 239 energy 7.376
    Minimum 5 at index 272 energy 9.648
    Minimum 6 at index 907 energy 11.366
    Minimum 7 at index 944 energy 0.630
    Minimum 8 at index 953 energy 2.415
    Minimum 9 at index 955 energy 4.343
    Minima sorted after energy
    Minimum 0 at index 90 energy 0.000
    Minimum 1 at index 198 energy 0.324
    Minimum 2 at index 944 energy 0.630
    Minimum 3 at index 953 energy 2.415
    Minimum 4 at index 955 energy 4.343
    Minimum 5 at index 239 energy 7.376
    Minimum 6 at index 272 energy 9.648
    Minimum 7 at index 82 energy 11.366
    Minimum 8 at index 224 energy 11.366
    Minimum 9 at index 907 energy 11.366

Best,
Miriam