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

From: Silvia Carlotto <silvia.carlotto.unipd.it>
Date: Mon, 12 Apr 2010 11:08:50 +0200

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!!!!

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Received on Mon Apr 12 2010 - 02:30:05 PDT
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