Hello,
On Fri, Jan 22, 2010 at 9:57 PM, Jagdeesh C <jagc666.gmail.com> wrote:
> Hi Nicholas,
>
> I loaded my prmtop (top) file first and then I loaded the mdcrd. It seems
> to show bad connections with unexpected lines when I did that. I will go
> through all the links and points you mentioned and verify that I have loaded
> the files appropriately. Thank you very much for your quick reply.
One thing to note, and excuse me if I'm pointing out the obvious, but
you're running your simulations with periodic boundary conditions (ntb
= 1 implies constant volume). Thus, the box information (extra
numbers) will be written to your mdcrd file at the end of each frame.
If you load the mdcrd as "amber coordinates", then the box information
will be interpreted as coordinates, and, as you can guess, everything
will desynchronize and you will get a mess.
You can get around this by selecting the "amber coordinates with
periodic box" information option. If this doesn't work, then I'm not
sure what else I'd try. Often, a mess with VMD implies some sort of
incompatibility between a coordinate file and a topology file (as long
as it's not a common mistake like the one mentioned above).
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 22 2010 - 22:30:03 PST
