[gmx-users] dihedral angle calculation of glycosidic bond

[Md. Imrul Reza Shishir]

Dear all
I want to calculate glycosidic bond torsion angle of simulation data. For
this purpose I execute "gmx angle" command with type dihedral selection.
And create the index file by "gmx make_ndx" command with proper atom
selection. Is this procedure is correct? As there is no data was listed in
angle.ndx when i execute "gmx mk_angndx" command.

*gmx make_ndx -f *.gro -o *.ndx* (with proper atom selection multiple of 4
i.e. a *O5 | a C1 | a O1 | a C4*)



*gmx angle -f *.xtc -n *.ndx -od *.xvg -ov *.xvg -type dihedral -periodic
yes *
*gmx mk_angndx *.tpr -n angle.ndx -type dihedral*

my question why there is no value of gmx mk_angndx? And index file from gmx
make_ndx is workable with gmx_angle?

there is a portion of gro file.

    1UN2     O5   20  10.335   7.227   9.575  0.1310  0.1464 -0.7432
    1UN2     C4   21  10.525   7.258   9.419 -0.2607 -0.7233  0.1164
    1UN2     H4   22  10.475   7.336   9.362 -0.9081 -1.1644  0.0725
    2UN1     O1   23  -0.335   7.263   9.437 -0.2866 -0.4682  0.2526
    2UN1     C1   24  -0.247   7.292   9.335  0.2174  0.1053  0.8414
    2UN1     H1   25  -0.261   7.225   9.250 -1.6085  0.1598  1.0644

..........................................................................................................................
    2UN1     O6   37  11.041   7.408   9.640 -0.3322  0.4500 -0.2078
    2UN1    HO6   38  11.094   7.330   9.643 -0.8978  0.0971  1.1878
    2UN1     C5   39  -0.040   7.355   9.432  0.1600 -0.0553  0.0341
    2UN1     H5   40   0.059   7.309   9.434  0.3506  0.3966  1.6282
    2UN1     O5   41  -0.115   7.260   9.359  0.2786 -0.2109  0.1156
    2UN1     C4   42  -0.034   7.489   9.359  0.5410  0.3820  0.8702
    2UN1     H4   43   0.024   7.557   9.423  2.1409 -0.2840  0.1838
    3UN1     O1   44   0.013   7.471   9.228 -0.6946 -0.5179  0.5289
    3UN1     C1   45   0.136   7.412   9.205 -0.1828  0.6716  0.0827
    3UN1     H1   46   0.122   7.304   9.203  0.1692  0.4707 -5.5831
    3UN1     C2   47   0.202   7.442   9.071  0.1712  0.1039  0.1261
    3UN1     H2   48   0.221   7.546   9.044  2.7417 -0.1823  0.6206
.................................................................................................................................
    3UN1    H62   57   0.296   7.370   9.531 -0.1078  0.0096 -0.9312
    3UN1     O6   58   0.463   7.277   9.512 -0.1867  0.3920 -0.7182
    3UN1    HO6   59   0.492   7.282   9.602  0.1895  0.7603 -0.8566
    3UN1     C5   60   0.322   7.350   9.325 -0.2264 -0.5776 -0.2885
    3UN1     H5   61   0.285   7.248   9.313  0.0998 -0.8705  1.0602
    3UN1     O5   62   0.222   7.449   9.307  0.5614  0.2131 -0.3764
    3UN1     C4   63   0.408   7.377   9.202 -0.1907 -0.1807 -0.1760


Thank you very much

best Regards
Md iMrul Reza Shishir