AMBER Archive (2006)

Subject: Re: AMBER: amber: problem in center command

From: Vlad Cojocaru (
Date: Fri Jan 20 2006 - 03:48:42 CST

Its not a center command problem, rather your trajectory file
C-C1-md2.mdcrd has a problem ..
Can you load the trajectory in vmd?

Obviously your trajectory file is corrupted ... I guess you should check
if you can load this file into a visualization program (vmd for
instance) and then check whether you have only 1 or several frames
corrupted or the entire file has a problem . If only several frames are
corrupted than you should use ptraj to remove those frames (see trajin,
trajout commands) and go on to the next step with the new trajectory ...

If the entire file is corrupt ... then I am afraid you should track the
problem somewhere in your MD run ...


xiphias xie wrote:

>Deal all:
> I am so sory to bother you again .
> Here is my scrip:
>trajin C-C-md1.mdcrd
>trajin C-C-md2.mdcrd
>trajout C-C-md.mdcrd
>center origin
>when I ran it , it display that :
>PTRAJ: trajin C-C1-md1.mdcrd
>Checking coordinates: C-C1-md1.mdcrd
>PTRAJ: trajin C-C1-md2.mdcrd
>Checking coordinates: C-C1-md2.mdcrd
>WARNING in checkCoordinates(): File is corrupted...
> '*' detected in AMBER trajectory (C-C1-md2.mdcrd)
>PTRAJ: trajout C-C1-md.mdcrd
>PTRAJ: center origin
>Mask [*] represents 6696 atoms
>PTRAJ: go
>Thank you for your attention!
> xiphias
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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