[gmx-users] problem with protein secondary structure analysis
minnale_gnos at rediffmail.com
Sun Aug 17 17:23:25 CEST 2008
Hi Shay and Justin Thanks for your clear suggestion
your suggested way is working fine.
Thanks alot once again.
On Sun, 17 Aug 2008 Shay Amram wrote :
>How big is your file?
>Technically you might not be able to load the file if it is larger than you
>One way to deal with this is converting the file (xtc or trr) not to include
>If that is indeed the case, I suggest you create a group that contains
>everything you have in the simulation except for the solvent and then run:
>trjconv -f file.xtc -o file_without_water.xtc -n index.ndx
>You will be asked to choose a group - choose the group you created without
>Now do the same to your .gro file (so there would be the same number of
>atoms in gro and in the xtc), and you should be able to load the entire
>"no-water" xtc without problems.
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>On Behalf Of minnale
>Sent: Sunday, August 17, 2008 08:30 AM
>Subject: Re: Re: [gmx-users] problem with protein secondary structure
>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
> >> trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000
> >> selected system, it showed
> >>Fatal error:
> >>Index 2726 is larger than the number of atoms in the trajectory file
> >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
> >>Thanks in advance.
> >>Rediff Shopping
>e-default.htm/1050715198 at Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUE
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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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