AMBER Archive (2004)

Subject: Re: AMBER: Defining residues

From: John Bushnell (bushnell_at_chem.ucsb.edu)
Date: Mon Feb 23 2004 - 14:44:44 CST

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 opitz_at_che.udel.edu 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,
>
> Armin
>
> ==============Original message text===============
> On Mon, 23 Feb 2004 11:49:58 EST "David A. Case" wrote:
>
> On Sat, Feb 21, 2004, opitz_at_che.udel.edu wrote:
>
> > set RES head RES.1.H1
> > set RES tail RES.1.H11
> > set RES tail RES.1.H12
>
> As I understand it, this won't work. The third command above will override
> what was done in the second command -- residues have only one "tail".
>
> ...regards...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
>
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