Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)...

From: Silvia Carlotto <silvia.carlotto.unipd.it>
Date: Mon, 12 Apr 2010 13:30:36 +0200

I used iwarp=1 so probabily it is not a problem connect with the diffusion.

With the command tail in unix I see the last part of the file and there is
not errors.

I tried these two input:

trajin inputfile.mdcrd 1 8000 5
strip :WAT
strip :Cl-
trajout outputfile.mdcrd

to save every 5 frame and jump the 7659 corrupted file but the analysis stop
at set 7659

and then, to save the part of the trajetory from 7660 to end I used this
input

trajin inputfile.mdcrd 7660 8000 5
strip :WAT
strip :Cl-
trajout outputfile.mdcrd

but the result does not change.

Is there a command to jump a frame?

thanks




2010/4/12 Jason Swails <jason.swails.gmail.com>

> How is it corrupted? Did you use iwrap=1 in your simulation input
> file? If not, I can imagine that starting at frame 7.659, one of the
> water molecules has diffused too far for the fixed-format output of
> the mdcrd to handle (and thus prints ***** for the coordinate). If
> this is the case, then every frame after 7.659 is probably corrupted.
>
> It would also be helpful to see your ptraj script when you tried to
> read in, for instance, every 5th frame. You may consider trying to
> read in the first 7.658 frames and printing those out and visualizing
> them to see what may be going on (i.e. if it is the diffusion problem
> i mentioned).
>
> Use the following trajin command:
>
> trajin inputfile.mdcrd 1 7658 1
> strip :WAT:Cl-
> trajout outputfile.mdcrd
>
> In the future, I suggest you try using netcdf trajectory files instead
> of ascii mdcrd files (see variable ioutfm in the amber manual to use
> this format in both sander and pmemd). Ptraj can read these files as
> well, and they are faster to write, read, and process, they hold
> higher precision numbers, and they are a fraction of the size. Also,
> if you do not have AmberTools1.3 installed, this version of ptraj may
> be useful in this problem (it only reads frames you intend to process,
> and so is much faster and will skip bad frames if you don't include
> them in analysis).
>
> Good luck!
> Jason
>
> On Mon, Apr 12, 2010 at 5:08 AM, Silvia Carlotto
> <silvia.carlotto.unipd.it> wrote:
> > Dear amber user,
> >
> > I have a big trajectory .mdcrd file (29G and 500.000 frames) and I want
> to
> > strip water molecules.
> >
> > The preview trajectory (29G) do not give me any problem but the second
> one
> >
> > give me this error in ptraj
> >
> >
> > Warning in readAmber trajectory():Set #7659 is corrupted (3.)...
> >
> >
> > The .out file does not give me some kind of errors and I used the restart
> > file of
> >
> > this simulation in other simutations without any errors.
> >
> >
> > My ptraj scrip is simply
> >
> > trajin inputfile.mdcrd
> > strip :WAT
> > strip :Cl-
> > trajout outputfile.mdcrd
> >
> > I try to:
> >
> > 1) save every 5 frames to jump the damege frame
> > 2) cut the trajectory and save the part after the corrupted frames
> >
> >
> > But every time the ptraj tool stop at #7659 frame.
> >
> > The time mahcine calculation is very long so I want to know if I can save
> in
> > some way my simulation.
> >
> > Is it possible to jump in same way the corrupted frame or to delate from
> the
> > mdcrd file?
> >
> > The file is too big to open it with a text editor.
> >
> > Plese help me!!!
> >
> > I have not other idea!!!!
> >
> >
> > silvia
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Silvia Carlotto, Ph.D
UniversitÓ degli Studi di Padova
Dipartimento di Scienze Chimiche
via Marzolo 1, 35131 Padova
Telefono: +390498275124
E-mail: silvia.carlotto.unipd.it
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Received on Mon Apr 12 2010 - 05:00:02 PDT
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