VMD-L Mailing List

From: Anshul Shah (aashah_at_bnl.gov)
Date: Mon Jul 28 2003 - 15:45:05 CDT

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