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

[David van der Spoel]

Eudes Fileti wrote:
> 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.
> 
>
you may need to add the -type flag, run g_sgangle -h


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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