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

From: X Sun <>
Date: Wed, 04 Sep 2013 18:22:21 -0600

Dear Thomas,

I tried to convert MDCRD to DCD, PBC information is still in DCD file. But there is no PBC information from dcd to mdcrd. With BOX or NOBOX parameter, the output files have no differences. What should I do??


Xiaoquan Sun.


X Sun

发件人:Thomas Cheatham <>
发送时间:2013-09-04 15:57
主题:Re: [AMBER] Convert DCD to MDCRD, lose PBC.
收件人:"AMBER Mailing List"<>

> 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 - 16:30:02 PDT
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