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

[Justin Lemkul]

On 3/12/14, 1:37 AM, Sathish Kumar wrote:
> 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 ] .
>

The dihedrals are grouped by type.  Phi is the phase angle, the next number is 
the multiplicity, then the force constant.

> 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.
>

Depending on how mk_angndx groups things, it may be exactly what you need.  But 
if some dihedrals correspond to different atoms but have the same parameters, 
you'll have to make each group manually (simple scripting) or with make_ndx, 
instead.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================