AMBER Archive (2006)

Subject: Re: AMBER: how to select the problematic residues(atoms) in VMD

From: Andres Palencia (
Date: Thu Oct 26 2006 - 06:56:31 CDT

Rachel wrote:
> Dear AMBER users,
> Hi! I am using VMD to view the trajectory from AMBER(the *.mdcrd
> file), from the movie, I can see some of the bonds became so stretched
> (became so far away from the protein), which obviously should not
> happen, however, how do I know which bonds are they, which residues
> they belong to so that I can look at them in more details? Thanks a
> lot for your help.
> Best regards,
> Rachel
Dear Raquel,

just to know which residues are responsible for the H-bonds observed,
you should go to mouse option in VMD and click label atom. Then pick on
the atom making the bond, and it will give you the atom and the residue
belonging to.
I f you are new user with VMD this link will be useful for you, I am new
user also:

good luck, andres...
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