Re: [AMBER] Fwd: Checking bonds commanded with leap

From: David A Case <>
Date: Mon, 5 Jan 2015 07:31:40 -0500

On Mon, Jan 05, 2015, Francesco Pietra wrote:

> I forgot to ask why VMD does not show the existing (according to leap and
> bonds between the protein backbone and the active center.

If you just load a pdb file into VMD, it has no knowledge of bonds, and makes
guesses based on distances. If you load the parm7 file, followed by
coordinates, you should see the bonds that are in the parm7 file.


AMBER mailing list
Received on Mon Jan 05 2015 - 05:00:02 PST
Custom Search