AMBER Archive (2006)

Subject: Re: AMBER: Question about LEAP and twisting a dihedral angle

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Sep 06 2006 - 03:46:57 CDT

Dear Dave,

Thanks for your suggestions. I wrote a script in PERL which puts a
particular structure in a specific orientation. I still used the impose
command to change the dihedral angles, but after having a unique
orientation, it was easy to create 360 structures whose atoms are
exactly at the same coordinates, except of those which are twisted.

If anyone needs to create a reference structure for a simulation and wants
to use this script, let me know. What it does is, it translates the 1st
atom to origin, rotates the structure such that the 2nd atom is on x-axis,
and then rotates the structure again to put the 3rd atom on x-y plane.
This is a unique structure which can be used for reference purposes.

Best,

On Sun, 3 Sep 2006, David A. Case wrote:

> On Sun, Sep 03, 2006, Ilyas Yildirim wrote:
> >
> > The tetramer has 2 strands and I am changing just one dihedral angle of
> > strand # 1 to zero. The new .pdb file (ggcc_new.pdb) is totally different.
> > Yes, it keeps this particular dihedral angle at zero degrees; but it
> > changes all of the atom positions of strand #1 while keeping the atom
> > positions of strand # 2 untouched. I know that what I am doing is not
> > right; I need to describe some more restraints to make leap understand
> > that strand #2 is part of the structure, and that it has to be helical,
> > but I am not sure how to do it.
> >
> > Right now, I am writing a script which is going to rotate a structure in a
> > particular orientation, and plan on doing some complicated procedures
> > to just change a dihedral angle. Its pretty time consuming and
> > therefore I am wondering if I can solve this problem with leap, using the
> > 'impose' command. Thanks in advance.
>
> NAB has a nice interface here, at least for some problems. It lets you
> specify which atoms are to move, as well has making it easy to construct and
> apply a rotation about an arbitrary axis. The (known) problem with "impose"
> is that it has to try to guess which atoms to move.
>
> I'm cc-ing this to Wei Zhang, so that maybe gleap will be smarter.
>
> ..thx...dave
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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