[gmx-users] Regarding 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.

It seems you only saved the first residue in your trajectory. If you
make matching trajectory and .tpr files that save the first ten
residues, then you should be able to proceed.

-Justin

Dear Justin

In brief I would like to tell you my problem. I have taken the atom numbers
those represent the dihedral angle atoms from the topology file to generate
the index file to generate .trr file. Then I have generated the another
index file for .gro file. As number of dihedral angles 36 for 18 residues,
I could save 24 atoms according to 2*N/3 formula. As my area of interest is
first 2-12 residues, I have taken numbers of backbone atoms in my index
file for resized.gro file. Then I executed the following command

trjconv -s foo.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0


Here I got the error as follow

> 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.

Now come to your suggestion, you suggested me that first make matching
trajectory and .tpr files for 10 residues. Here I not able to getting how
does that work. Because we have to generate the .trr file based on the
dihedral index file, which means definitely I will get the same error.
Kindly tell me more about how to generate the resized.gro file for first 10
residues.

Thanks in advance



Surya
Graduate student
India.