[gmx-users] cannot successfully finished the dPCA

[Seera Suryanarayana]

Dear gromacs users

I done simulations of peptide of 20 residues length for 300ns. As I would
like to explore the conformational flexibility I have chosen to do dPCA. I
have gone through the tutorial which is present in the gromacs cite.
Firstly, I have created the index file which shows the dihedral angle atom
numbers. I have given the 36 dihedral angles information of 18 residues.
Based on the formula 2*N/3 for 24 atoms I can create index file which can
be used in the neat step to create the .gro file. In my index file I gave
first 24 backbone atoms numbers. When  use the gmx trjconv for getting
resized.gro I got following error.

Fatal error:
Index[4] 25 is larger than the number of atoms in the
trajectory file (24). There is a mismatch in the contents
of your -f, -s and/or -n files.

I got error meaning. In my index file fifth element is 25 which is greater
than the total number of atoms number that is 24. If I give first 24
numbers Then I got .gro file only for first file as follow.

Generated by trjconv : Protein in water t=   0.00000
   24
    1LYS      N    1  -0.370  -0.929   0.912
    1LYS     H1    2   0.411   0.167  -0.986
    1LYS     H2    3  -0.533   0.846  -0.352
    1LYS     H3    4  -0.936  -0.603   0.798
    1LYS     CA    5   0.049  -0.999  -1.000
    1LYS     HA    6  -0.003   0.264  -0.965
    1LYS     CB    7   0.935  -0.356   0.188
    1LYS    HB1    8  -0.982   0.862  -0.506
    1LYS    HB2    9   0.358  -0.934   0.839
    1LYS     CG   10  -0.544   0.010  -1.000
    1LYS    HG1   11  -0.646   0.763  -0.335
    1LYS    HG2   12  -0.942  -0.930  -0.367
    1LYS     CD   13   0.374  -0.927  -0.662
    1LYS    HD1   14   0.750   0.341  -0.940
    1LYS    HD2   15  -0.661   0.751  -0.775
    1LYS     CE   16  -0.632  -0.591   0.807
    1LYS    HE1   17  -0.561   0.828   0.693
    1LYS    HE2   18   0.721   0.610  -0.793
    1LYS     NZ   19  -0.410   0.912  -0.585
    1LYS    HZ1   20  -0.811  -0.419   0.908
    1LYS    HZ2   21   0.054  -0.999  -0.159
    1LYS    HZ3   22   0.987   0.203  -0.979
    1LYS      C   23   0.749  -0.663  -0.820
    1LYS      O   24  -0.573  -0.900   0.436
   2.00000   2.00000   2.00000

But I want to get the information for first 10 residues of my peptide.
Kindly tell me how to do get dPCA for first ten residues of my 20 residues
simulated peptide.

Thanks in advance
Surya
Graduate student
India.