From: John Stone (
Date: Thu Jul 31 2003 - 11:44:38 CDT

Dear Anshul,
  Can you email me a copy of the file that gave you problems?
I'd like to see what is different about that CRD file. Sorry I didn't
reply to you earlier, I'm out of town at Siggraph this week, and
today is the first day I've had good enough network connectivity to
do anything but minimal email.

  John Stone

On Mon, Jul 28, 2003 at 06:17:29PM -0400, Anshul Shah wrote:
> The problem has been fixed: I needed to remove the top line of the crd
> file. I hadn't known that that was necessary.
> Anshul Shah wrote:
> > Hi all,
> >
> > I am a new user of VMD and Amber. I am having a problem that sounds
> > similar to something I read in the list archives. When I try to open
> > Amber 7.0 format .prmtop and .inpcrd files in VMD 1.8.1, the molecule I
> > get is very much distorted; that is, the bonds are very obviously not in
> > their proper configuration. The original .pdb file looks fine in VMD,
> > but I get this problem after using Amber Leap to generate the .prmtop
> > and .inpcrd files. It seems that either Leap went wrong, or VMD is not
> > using the two files correctly. Does anyone what this problem might be,
> > or how I can fix it?
> >
> > Thanks,
> > Anshul

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