[gmx-users] problem with protein secondary structure analysis

minnale minnale_gnos at rediffmail.com
Sun Aug 17 07:30:10 CEST 2008

Thanks to Justin for his prompt reply
in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I am in doubt that first 250ps of md run it in npt condition later nvt till 7ns finally made into long .xtc file.
I tried your suggested way in earlier post but I didnt get it. 

one more doubt I am having is
If I load entire .xtc file which contain 7ns trajectory it didnt load   
Could please tell me why its not loading 
Thanks in advance.

On Sat, 16 Aug 2008 Justin A.Lemkul wrote :
>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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