[gmx-users] problem with protein secondary structure analysis

[minnale]

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
>machine's memory.
>
>One way to deal with this is converting the file (xtc or trr) not to include
>solvent.
>
>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
>the water.
>
>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.
>
>
>
>-Shay
>
>
>
>   _____
>
> 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
>To: gmx-users1
>Subject: Re: Re: [gmx-users] problem with protein secondary structure
>analysis
>
>
>
>
>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.
> >
> >-Justin
> >
> >>
> >>Could you please give me suggestion if any one have experienced this type
>of problem
> >>Thanks in advance.
> >>
> >>
> >>
> >>Rediff Shopping
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> >>
> >>
> >>------------------------------------------------------------------------
> >>
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> >-- ========================================
> >
> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul[at]vt.edu | (540) 231-9080
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >========================================
>
>
>
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