[gmx-users] Regarding calculation of torsion angles in DNA

[Sathish Kumar]

Hai

        I am trying to calculate torsional angles in DNA, for that first I
made angle.ndx file by using

mk_angndx -f prod.tpr -n angle.ndx -type dihedral

the out put angle.ndx is looks like as following

[ Phi=0.0_3_1.31 ]
    12     2     3     4    12     2     3    15    12     2     3    16
     5     6     7     8    21     6     7     8    22     6     7     8
     6     7     8     9     6     7     8    10     6     7     8    11
    23     7     8     9    23     7     8    10    23     7     8    11
    24     7     8     9    24     7     8    10    24     7     8    10
    24     7     8    11    38    28    29    30    38    28    29    41
    38    28    29    42    31    32    33    34    47    32    33    34
    48    32    33    34    32    33    34    35    32    33    34    36
    32    33    34    37    49    33    34    35    49    33    34    36
    49    33    34    37    50    33    34    35    50    33    34    36
    50    33    34    36    50    33    34    37    64    54    55    56
    64    54    55    67    64    54    55    68    57    58    59    60

[ Phi=0.0_3_1.34 ]
    13     2     3     4    14     2     3     4     2     3     4    17
     2     3     4    18    15     3     4     5    16     3     4     5
     3     4     5    19     3     4     5    20    17     4     5     6
    18     4     5     6     4     5     6    21     4     5     6    22
    19     5     6     7    20     5     6     7     5     6     7    23
     5     6     7    24    39    28    29    30    40    28    29    30
    28    29    30    43    28    29    30    44    41    29    30    31
    42    29    30    31    29    30    31    45    29    30    31    46
    43    30    31    32    44    30    31    32    30    31    32    47
    30    31    32    48    45    31    32    33    46    31    32    33
........................

What is the meaning of [ Phi=0.0_3_1.34 ] .

I want to find the changes in the torsion angles alpha, beta,
gammaa.......etc through out the simulation.

For this how can i make the index file.

Thank You very much.




-- 
regards
M.SathishKumar