AMBER Archive (2006)

Subject: Re: AMBER: problem in center command

From: xiphias xie (
Date: Fri Jan 20 2006 - 19:30:44 CST

Thank you very much!

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

No, I can not load the trajectory in vmd completely.
the corruption is in the same point .

> 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 ...
I can not understand that my mdcrd file is corrupt,
but my out file has no problem. I am trying....


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