VMD-L Mailing List

From: Anshul Shah (aashah_at_bnl.gov)
Date: Mon Jul 28 2003 - 17:17:29 CDT

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