[gmx-users] no groups in indexfile!

[Justin Lemkul]

On 10/15/12 1:03 PM, Amir Abbasi wrote:
> tnx But I need these two planes angle too.
> what should I do?
> can I convert all of trajectory file to pdb?
> in order to do these manually?
>

That would be extremely inefficient.  Determining what's wrong with your index 
file is probably a much better solution.

-Justin

>
> --------------------------------------------------------------------------------
> *From:* Justin Lemkul <jalemkul at vt.edu>
> *To:* Amir Abbasi <amir.abbasi69 at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *Sent:* Monday, October 15, 2012 7:47 PM
> *Subject:* Re: [gmx-users] no groups in indexfile!
>
>
>
> On 10/15/12 11:48 AM, Amir Abbasi wrote:
>  > Hi !
>  > I want to use g_sgangle to find distance between two groups (each group
> includes 3 atoms).
>  > I use this command:
>  > g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od
> 12_dist.xvg
>  > but i got this error
>  > Fatal error:
>  > Error: no groups in indexfile
>  >
>  > my index file:
>  >  [ G3 ]
>  > 76    81    85
>  >  [ G4 ]
>  > 110    115    119
>  >
>
> The most likely explanation is that you have some problem with non-Unix line
> endings in the file.  Note that if you just need distances between groups,
> g_dist is more efficient for that calculation.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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