Dear Dr. Swails,
I appreciate your kind advice.
> He is talking about coordinates here. The easiest way to obtain the
It makes sense.
Thank you for usual support.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Friday, March 08, 2013 10:08 PM
To: AMBER Mailing List
Subject: Re: [AMBER] impose for improper torsion: from I. Kurisaki
On Fri, Mar 8, 2013 at 6:46 AM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Professor Yevs,
>
> Thank you for your advices!
>
> > x -> -x should do the job...
> I'd like to try that but
> Would you let me know what means x and -x here?
> I guess it as an order of atoms or value of DHA,
> but still being confusing.
>
He is talking about coordinates here. The easiest way to obtain the
inverse stereoisomer of a chiral compound is to reflect it in _some_ plane
(any plane). One plane that satisfies the condition of _some_ plane is the
y,z-plane. Reflecting a molecule in the y,z-plane converts the point x,y,z
-> -x,y,z. Ergo, by replacing all X-coordinates with the negative value
will generate the stereoisomer. Likewise, you could reflect in the x,y-
plane (x,y,z -> x,y,-z) or the xz-plane, etc.
In the AMBERHOME/AmberTools/test/leap directory there is a test file that
actually inverts the chirality of a GLU residue (by reflecting in the
x,y-plane) using the following command (see Run.cmds)
dglu = copy GLU
transform dglu {{1 0 0} {0 1 0} {0 0 -1}}
d_amino = sequence {ACE dglu NME}
This creates a copy of the GLU residue (so you don't invert the original),
reflects it in the xy-plane (notice it makes the Z-coordinate negative)
then generates a capped amino acid of D-GLU.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 08 2013 - 06:00:05 PST
