On Mon, Jun 17, 2013 at 7:07 PM, Yan Duan <yduan1.ualberta.ca> wrote:
> Dear Amber users:
> Hi, currently I'm kind of learning the AMBER software, and I started from
> the tutorials on its website. Today when I tried to run the TUTORIAL A16:
> Lipid Bilayers with an Amber Lipid Force
> Field<
> http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html
> >,
> everything went well except one issue: when I tried to view the trajectory
> files, I loaded the *.prmtop file first, it was fine, then I loaded the
> *.mdcrd, but nothing came out in VMD and in linux terminal it showed like:
>
> Using plugin crdbox for coordinates from file
> /home/yan/Desktop/amberfiles_local/DOPC_128_02_Heat.mdcrd
> Problem reading CRD file
> Info) Finished with coordinate file
> /home/yan/Desktop/amberfiles_local/DOPC_128_02_Heat.mdcrd.
>
> I wonder that is this error because of the wrong command lines from the
> tutorial, or VMD itself? how could I view its trajectories then?
>
> So many thanks for your time and generous help!
>
The lipid tutorial sets the variable "ioutfm=1" in the input file. This
indicates that the trajectories should be written in NetCDF format. (If you
make the extension '.nc' then VMD will automatically recognize its format).
Try choosing "NetCDF (AMBER, MMTK)" as the file type.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 20 2013 - 04:30:02 PDT
