AMBER Archive (2004)

Subject: Re: AMBER: Defining residues

From: opitz_at_che.udel.edu
Date: Mon Feb 23 2004 - 15:47:51 CST

('binary' encoding is not supported, stored as-is) Also, when defining these residues. When in the defined residue the
carbon atom does not have any electronwithdrawing groups attached, but in
the bonded state it does, how do you define the hydrogens, as h1 or hc?

==============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 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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