Brian,
Thanks very much. Viewing the restart files makes things rational.
Heather
> Date: Thu, 17 Jan 2013 15:32:33 -0500
> From: radak004.umn.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] difficulty with basic tutorial 1
>
> Heather and Dan,
>
> In my experience, neither of those plugins reliably work as expected. I
> always use "Amber7 Restart" (-rst7 on the command line or give files the
> "rst7" file extension). That seems to work for all restart files as well as
> inpcrd files from Leap, regardless of whether or not periodic boundary
> conditions are used.
>
> Regards,
> Brian
>
> On Thu, Jan 17, 2013 at 2:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Thu, Jan 17, 2013 at 11:50 AM, <mhclewett.msn.com> wrote:
> > > ... with the coordinates looking like a child's scribble (picture below)
> >
> > I didn't see any picture attached, but what you describe sounds like
> > maybe when you are visualizing the trajectory that the number of atoms
> > in the topology file doesn't match the trajectory file. It could also
> > happen if you load an Amber trajectory that has box coordinates with
> > "Amber Coordinates" instead of "Amber Coordinates with Periodic Box".
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
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Received on Fri Jan 18 2013 - 07:30:03 PST
