Re: [AMBER] Convert DCD to MDCRD, lose PBC.

From: Thomas Cheatham <>
Date: Wed, 4 Sep 2013 14:57:56 -0600 (Mountain Daylight Time)

> I tried to use ptraj to convert DCD file output from NAMD to MDCRD
> format for easy reading by my codes, however, it looks the process loses
> the PBC information. When I use VMD to convert DCD into CRDBOX format,
> there is PBC information in CRDBOX. I checked the default option of
> ptraj is nobox. Does someone may clarify how I could set up with box or
> PBC for trajout?

I believe the default format is to add box information, i.e. to get
it not to output the box information you add "nobox". If "nobox" is
specified on your command line, remove it.


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Received on Wed Sep 04 2013 - 14:00:04 PDT
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