[gmx-users] Re: gmx-users Digest, Vol 33, Issue 69

[Eudes Fileti]

I am trying to calculate the angle between two plans.
For this I created an index file with all triples of atoms related to
each plan.
Thus I would get the angle between the normal of these plans.
To get the index file I used:

mk_angndx -s topol.tpr -n angle.ndx

To calculate the angles I used

g_sgangle -f traj.xtc -n angle.ndx -s topo.tpr -oa sg_angle.xvg

However I obtained the following error.
Anyone could say me as to overcome this?
thanks
eef



Reading file term.tpr, VERSION 3.3 (single precision)
Group     0 (Theta=108.0_334.72) has   180 elements
Group     1 (Theta=120.0_585.76) has   360 elements
Group     2 (Theta=110.7_313.8) has 15000 elements
Group     3 (Theta=107.8_276.144) has 12000 elements
Group     4 (Theta=109.5_418.4) has  3000 elements
Group     5 (Theta=108.5_460.24) has  3000 elements
Group     6 (Theta=109.5_292.88) has  6000 elements
Select a group: 0 4
Selected 0: 'Theta=108.0_334.72'
Select a group: Selected 4: 'Theta=109.5_418.4'

Group Theta=108.0_334.72 contains the following atoms:
Atomname 0: C3
Atomname 1: C1
Atomname 2: C9
Atomname 3: C4
Atomname 4: C2
Atomname 5: C10
Atomname 6: C1
Atomname 7: C3
Atomname 8: C5
...

Atomname 177: C40
Atomname 178: C60
Atomname 179: C45

Group Theta=108.0_334.72 contains the following atoms:
Atomname 0: C3
Atomname 1: C1
Atomname 2: C9
Atomname 3: C4
Atomname 4: C2
Atomname 5: C10
Atomname 6: C1
....
Atomname 177: C40
Atomname 178: C60
Atomname 179: C45

Careful: distance only makes sense in some situations.

Reading frame       0 time    0.000
Back Off! I just backed up sg_angle.xvg to ./#sg_angle.xvg.2#
-------------------------------------------------------
Program g_sgangle, VERSION 3.3
Source code file: gmx_sgangle.c, line: 127

Fatal error:
Something wrong with contents of index file.

-------------------------------------------------------

"It's So Fast It's Slow" (F. Black)


_______________________________________
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166
CEP 09210-170
skype: eefileti