[gmx-users] problem with protein secondary structure analysis

minnale minnale_gnos at rediffmail.com
Sat Aug 16 15:48:13 CEST 2008

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)

Could you please give me suggestion if any one have experienced this type of problem
Thanks in advance.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080816/0931834b/attachment.html>

More information about the gromacs.org_gmx-users mailing list