[gmx-users] problem with protein secondary structure analysis
minnale_gnos at rediffmail.com
Sat Aug 16 15:48:13 CEST 2008
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
Index 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.
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