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

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 12 Apr 2010 07:35:12 -0400

what exactly does ptraj say when it first checks the file? it should tell
you how many frames it thinks are present. only later will it say if one is
corrupted.

On Mon, Apr 12, 2010 at 7:30 AM, Silvia Carlotto
<silvia.carlotto.unipd.it>wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 12 2010 - 05:00:03 PDT
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