it also may be that you are not using the right format for
the trajectory (make sure to pick Amber coordinates and
you need to know if you have periodic box info in the file).
also make sure the pdb is the SAME MOLECULE as
your trajectory - meaning the atoms are in the same order.
it might be more reliable to use the prmtop first (load as
Amber7 parm for Amber 7/8/9) and then load the trajectory
as Amber coordinates (with periodic box if it is there).
I didn't see the original post so I don't know exactly what you tried.
On 7/12/07, David A. Case <case.scripps.edu> wrote:
> On Thu, Jul 12, 2007, M. Maeda wrote:
> >
> >
> > I check the resulted trajectory files by using VMD. Some very long bonds
> > assigned to protein (the color is gray and blue) could be seen between the
> > outside and the inside of the protein.
>
> Are you sure that "test.pdb" is a good structure? Were any of these
> long bonds present before you started? If not, try to figure out exactly
> which bonds are causing the problem. Run a short simulation (say 100 steps),
> set ntpr to 1 to get lots of print-out, and study the results carefully.
>
> ...good luck...dac
>
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Received on Sun Jul 15 2007 - 06:07:26 PDT
