VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 17 2007 - 22:24:58 CDT

Hi,
  I'd suggest asking the PBCTools plugin authors about the
correct way to do this given that the rotations you're performing
seem to be conflicting (at least from your description) with the
operations done by the PBC plugin in the calls your making.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 09, 2007 at 02:02:34PM +0200, Matteo Guglielmi wrote:
> Dear All,
>
> recently I did try to rotate a protein fully
> solvated by water molecules using the 'pcb'
> plugin and the following simple script:
>
> # pdb file header:
> # CRYST1 111.108 98.438 115.981 90.00 90.00 90.00
> set sys [mol new RUN01.pdb]
> set all [atomselect $sys all]
> set com [measure center $all]
> # 55.5484428406 49.2036247253 58.0394554138 ('set com...' outcome)
> $all moveby [list -55.5484428406 -49.2036247253 -58.0394554138]
> pbc set {111.108 98.438 115.981 90.00 90.00 90.00} -now
> pbc box -center origin
> set delta_deg 0.01
> # rotate x by -15 deg
> for {set x 0} {$x>-15} {set x [expr {$x - $delta_deg}]} {
> $all move [transaxis x -$delta_deg]
> pbc wrap -center origin
> }
> # rotate y by 40 deg
> for {set x 0} {$x<40} {set x [expr {$x + $delta_deg}]} {
> $all move [transaxis y $delta_deg]
> pbc wrap -center origin
> }
> # rotate z by -55 deg
> for {set x 0} {$x>-55} {set x [expr {$x - $delta_deg}]} {
> $all move [transaxis z -$delta_deg]
> pbc wrap -center origin
> }
> $all writepdb rotated.pdb
>
>
> .... well, the pbc box was correctly placed
> on top of the simulation box (volume) but
> the resulting 'rotated.pdb' was not good at
> all (water molecules close to the box edges
> got wrongly placed in the 'rotated.pdb' file)
>
> To see the weird effect just try the script with
> a simple water box.
>
> Do you know any better way to rotate a box
> with the pbc plugin?
>
> Best,
> MG. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078