Re: [AMBER] difficulty with basic tutorial 1

From: Brian Radak <radak004.umn.edu>
Date: Thu, 17 Jan 2013 15:32:33 -0500

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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>



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 Brian Radak                                             :     BioMaPS
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Received on Thu Jan 17 2013 - 13:00:03 PST
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