AMBER Archive (2004)

Subject: Re: AMBER: Defining residues

Date: Mon Feb 23 2004 - 15:35:44 CST

('binary' encoding is not supported, stored as-is) Sorry, I am thinking in steps today. The previous residues I used to read
in a pdb file, but looking at the pdb output from that, there is a
mistake. Now, my question is, if I follow the description below, how do I
connect the respective residues in leap? How do I make one molecule out
of it that I can then define as a new residue to attach something else too?


==============Original message text===============
On Mon, 23 Feb 2004 15:44:44 EST John Bushnell wrote:

I built some polymers with a tetrahedral core where I needed to
make a series of connections to the central unit. What I did
was to define a tail, connect a side-chain to it, then redefine
another tail, connect to that, etc. I believe that you can define
a tail as many times as you want, but it will be set to whatever
the last atom you set it to. As already suggested, 'desc' is your
friend in leap.

    - John

On Mon, 23 Feb 2004 wrote:

> I did find the problem that I had, but I still have 2 tails in the
> residue and it doesn't give me an error. Is it possible that residues can
> have 2 tails or is it just not telling me that there is a problem?
> Also, if I can only define one tail, how can I effectively make a residue
> that has 2 tails?
> Thanks,

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