AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 26 2006 - 10:26:22 CDT

Dear Rachel,

You might also find the following tutorial helpful:
http://amber.scripps.edu/tutorials/basic/tutorial2/

See section 8 for details on selecting atoms, bonds etc.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Andres Palencia
> Sent: Thursday, October 26, 2006 04:57
> To: amber_at_scripps.edu
> Subject: Re: AMBER: how to select the problematic
> residues(atoms) in VMD
>
> 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:
> http://bioweb.pasteur.fr/docs/doc-gensoft/vmd/vmd_help.html
>
> good luck, andres...
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