[gmx-users] problem with protein secondary structure analysis

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Aug 17 07:54:37 CEST 2008

Hi Minnale,

We do appreciate that english is not your native language (it isn't
mine either), but please try to write correct, complete sentences.
That will make it easier to read your posts, understand what you did
and where you went wrong and how we can, maybe, provide you a

Justins reply was right on, and you didn't read his post carefully
enough. He said to check your xtc-grps, not your tc-grps. xtc-grps, as
it is unambiguously explained in the manual, determines which sets of
atoms are saved to the .xtc file. To avoid such confusion, make it a
habit to paste the .mdp file when you post a problem (after having
checked the manual, the wiki, and the archives of the list, that is).



On Sun, Aug 17, 2008 at 7:30 AM, minnale <minnale_gnos at rediffmail.com> wrote:
> 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.
>>>Rediff Shopping
>>> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
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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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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