AMBER Archive (2008)

Subject: Re: AMBER: adding missing residues

From: David A. Case (
Date: Thu Jul 24 2008 - 10:37:36 CDT

On Thu, Jul 24, 2008, soumick wrote:
> Could you please tell me how can i add missing residues in amber? My
> protein has got two Chain A and B. I have some missing residues. I tried
> adding the residues in CAChe, but it is seperating the chains appart. The
> missing residues are begining of the chain A and B.

Do you mean: "how can I find the coordinates of residues that are not present
in the PDB file?"

What you need for that is probably a homology modeling program, or something
similar. Amber has a very limited ability to fill in missing coordinates, and
generally assumes that you know what the starting configuration will be. If
CAChe is not working for you, you probably need to figure out what its problem
is, or look into other model-building programs. Without knowing what the
"some missing residues" are, or even how many of them you have, it's hard to
be very specific with advice.


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