AMBER Archive (2006)

Subject: Re: AMBER: AMBER - leap - problems with impose command

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Dec 17 2006 - 02:45:13 CST

Sorry about the wrong explanation. After double checking one of the
projects I have done long time ago, here is the right procedure:

1. I wrote a .pl script, which translates/rotates any structure in a
particular orientation. For instance, if the original structure is a ggcc
helix, and the dihedral angle that is changed is the alpha-dihedral
angle of the first strand's 3rd and 4rd residue (cytosine-cytosine), then
the 1st residue of the 1st strand is untouched. If the N9 of G1 is
translated to origin, C8 is rotated on the x-axis, and C4 is rotated on
the x-y plane, then this is a unique orientation for this structure.

2. Let's say your structure in interest is called molecule.pdb. Using such
a script like this, bring this structure to a unique orientation. Call the new
structure molecule_orient.pdb. Save each strands as strand1.pdb and
strand2.pdb.

3. Let's assume that you change the dihedral angle of a particular bond in
the 1st strand. Let's also assume that you create 360 structures, with 1
degree increments. Create those structures in Leap using the 'impose'
command.

4. Using the script, you re-orient each of this 360 structures to this
particular orientation. Save them like strand1_(angle)_orient.pdb.

5. Combine each strand1_(angle)_orient.pdb files with strand2.pdb.

That is how I created my structures. Good luck,

On Sat, 16 Dec 2006, Piotr Cieplak wrote:

>
> No, it does not work that way.
> Piotr
>
>
> On Sat, 16 Dec 2006, Ilyas Yildirim wrote:
>
> > Date: Sat, 16 Dec 2006 06:17:22 -0500 (EST)
> > From: Ilyas Yildirim <yildirim_at_pas.rochester.edu>
> > Reply-To: amber_at_scripps.edu
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: AMBER - leap - problems with impose command
> >
> > My solution with impose is this:
> >
> > 1. Load the .pdb file in Leap and save it as temp.pdb.
> > 2. Remove the second strand strand from temp.pdb (which does not have any
> > dihedral change), and save the rest of the file as temp1.pdb.
> > 3. Save the removed part of the temp.pdb (namely the second strand) as
> > temp2.pdb.
> > 4. Load the temp1.pdb in Leap, and use the 'impose' command to change the
> > dihedral angles. Save the file as temp3.pdb
> > 5. Combine temp2.pdb with temp3.pdb; call it temp_final.pdb.
> >
> > Hope this helps. Best,
> >
> > On Fri, 15 Dec 2006, Piotr Cieplak wrote:
> >
> >> Also - there is another problem. If I have a monomer only - and try to
> >> change a diedral angle - then the whole molecule moves out of its initial
> >> position in space. It never happens in old EDIT program. And sometimes it
> >> is important for some application.
> >> P.
> >>
> >>
> >> On Sat, 16 Dec 2006, FyD wrote:
> >>
> >>> Date: Sat, 16 Dec 2006 07:22:36 +0100
> >>> From: FyD <fyd_at_u-picardie.fr>
> >>> Reply-To: amber_at_scripps.edu
> >>> To: amber_at_scripps.edu
> >>> Subject: Re: AMBER: AMBER - leap - problems with impose command
> >>>
> >>> Quoting Piotr Cieplak <cieplak_at_cgl.ucsf.edu>:
> >>>
> >>>> I am having problems with understanding why tleap changes orientation of
> >>>> the coordinates of the molecule in space after changing internal
> >>>> coordinates by impose command.
> >>>> When I have a dimer and do impose on one residue belonging to the first
> >>>> chain
> >>>> - then this first chain changes orientation in space destroying the
> >>>> whole complex,
> >>>> The coordinates of the second chain stay intact.
> >>>> The question is - what is the trick to keep the whole complex intact?
> >>>
> >>> I wonder if it is not a normal feature, I mean in LEaP. I might be wrong but
> >>> I wonder if the same thing also appends with 2 DNA strands... It appends also
> >>> in InsightII (Accelrys Inc). My understanding of this is that each time you
> >>> move an atom a part remains fix and another moves. I guess if you have no
> >>> chemical bond between your two chains, it is normal the second one does not
> >>> move if you change the 1st one. I think if your 2 chains were bounded it
> >>> would be different. What about trying this sequence ?
> >>>
> >>> - load your structure in LEaP
> >>> - Create a temporary bond between your 2 chains/change the molecule topology
> >>> - do your impose command
> >>> - remove the temporary bond created/rebuild the initial topology
> >>>
> >>> regards, Francois
> >>>
> >>>
> >>> -----------------------------------------------------------------------
> >>> The AMBER Mail Reflector
> >>> To post, send mail to amber_at_scripps.edu
> >>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>
> >>
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
> > ---------------------------------------------------------------
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu