On Wed, Sep 4, 2013 at 8:22 PM, X Sun <egeh00.aol.com> wrote:
> 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??
>
Try using cpptraj instead of ptraj...
>
> Thanks,
>
> Xiaoquan Sun.
>
> 2013-09-04
>
>
>
> X Sun
>
>
>
> 发件人：Thomas Cheatham <tec3.utah.edu>
> 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"<amber.ambermd.org>
> 抄送：
>
>
> > 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.
>
> --tec3
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 04 2013 - 17:00:03 PDT
