VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 23 2007 - 14:30:22 CDT

Hi,
  If you're using the orient script from the VMD script library,
I think that all you need to do to reorient the whole system
rather than just the ligand is to crate a new atom selection
for the whole system, and apply the orientation matrix to the
whole thing rather than jus the ligand selection.
The previous steps from the orient script would be followed as usual
except that you apply all of the "move" commands to the selall
selection rather than to the $sel selection which is what I'm assuming
was your ligand only, e.g.:
  set selall [atomselect top all]
  $sel move $A

I'm assuming you were using this orient script/package:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 08, 2007 at 09:36:49PM -0600, pkmukher wrote:
> Hello VMD users
>
> I am a new user of VMD. I want to carry out a particular
> orientation operation on my molecule(protein-ligand complex)
> In my case the ligand is situated in a cavity on the
> surface of the protein. I intend to carry out a steered
> molecular dynamics study. For this i require the
> protein-ligand complex to be oriented such that the force
> vector from the protein atom to the ligand atom be parallel
> to two of the axis. That way when i construct the solvent
> box i can keep it more elongated on the third axis to
> accomodate for the ligand movement once it comes out of the
> binding site.
> As an alternative I tried to use the orient script which
> orients on the basis of principle moments but i was not
> successful. Is there a way to define the principle moments
> on the basis of the ligand but carry out the reorientation
> for the whole complex. Currently when i defined the
> principle axis on the basis of the ligand it reoriented only
> the ligand.
>
> Thanks so much
>
>
> Prasenjit Kumar Mukherjee
> Graduate Student
> Department of Medicinal Chemistry
> School of Pharmacy
> University of Mississippi
> USA
>
> Cell - 662 380 0146
> Office - 662 915 1286
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078