you need to be more specific about what you are doing in VMD. you are
probably not choosing the right input format. if you are using a
recent version of Amber, use amber7 prmtop for the prmtop, then amber
coordinates or amber coordinates with box for the trajectory,
depending on whether it is PBC or not. if these don't help, but very
specific about what you are doing.
On Mon, Oct 4, 2010 at 7:04 AM, subrata paul <paul.subrata34.gmail.com> wrote:
> Dear sir
>
> I am simulating 10 disaccharide and 1000 water molecule. I done MD
> simulation.when I see the xxxx.prmtop and xxxxx.mdcrd in VMD it gave a bad
> structure ( looks like some line) .But when I see the minimized pdb {
> converting xxxx.rst to xxxx.pdb } , it look like a good structure . Why it
> is happen??? please help me regarding this.
>
>
> thanking you
> subrata
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Received on Mon Oct 04 2010 - 04:30:06 PDT
