[gmx-users] problem with protein secondary structure analysis

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 16 17:36:12 CEST 2008

minnale wrote:
> Hi all,
>     I intersted in analysing secondary structure of protein by using VMD 
> and performed these steps.
> 1. First loaded min.gro file and corresponding min.xtc then all  
> equalibration .xtc files till here MD movie has run fine.
> 2. I had long trajectory in a single file, so cut it down into 
> subtrajectories with 1ns interval by using *trjconv command and issued 
> like this
>   trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000
>   selected system, it showed
> Fatal error:
> Index[2725] 2726 is larger than the number of atoms in the trajectory 
> file (2725)

You've only saved a subset of your trajectory.  Check the xtc-grps in your .mdp 
file.  You can use trjconv if you have a reference structure that matches the 
contents of your trajectory.


> Could you please give me suggestion if any one have experienced this 
> type of problem
> Thanks in advance.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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