[gmx-users] Re: gmx-users Digest, Vol 33, Issue 69
Eudes Fileti
fileti at ufabc.edu.br
Sun Jan 28 15:40:51 CET 2007
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
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