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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>
--
================================ 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
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Jan 17 2013 - 13:00:03 PST
