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

From: Jason Swails <>
Date: Mon, 12 Apr 2010 06:03:35 -0400

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!

On Mon, Apr 12, 2010 at 5:08 AM, Silvia Carlotto
<> 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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Apr 12 2010 - 03:30:03 PDT
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