[gmx-users] how to optimize the orientation of the protein in a dodecahedron

[Thomas Evangelidis]

Hi Tsjerk and Erik,

Thanks for the comments. It's strange, because I get different minimum
distance for different orientations of the same protein structure using the
afore-mentioned command lines. I used a single step energy minimization for
speed (em_real.mdp). Below are the outputs of editconf and the last lines
of the output .gro files. There are differences in the Volume (884.007 nm^3
versus 996.803 nm^3), system size, center, box vectors, box volume, and
shift. What do these differences mean? Can they explain the different
mindist I get?

##
## Protein Orientation 1 editconf_4.5.5 output:
##

Read 17463 atoms
Volume: 884.007 nm^3, corresponds to roughly 397800 electrons
No velocities found
    system size :  9.205  8.440 11.378 (nm)
    diameter    : 12.498               (nm)
    center      :  6.524  6.242  9.385 (nm)
    box vectors :  9.205  8.440 11.378 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 884.01               (nm^3)
    shift       :  3.226  3.508 -4.789 (nm)
new center      :  9.750  9.750  4.596 (nm)
new box vectors : 13.000 13.000 13.000 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1553.51               (nm^3)


## Last line of the output .gro file:
  13.00000  13.00000   9.19239   0.00000   0.00000   0.00000   0.00000
6.50000   6.50000

## g_mindist output:

Last frame          0 time    2.000

The shortest periodic distance is 1.5735 (nm) at time 2 (ps),
between atoms 992 and 8506


##
## Protein Orientation 2 editconf_4.5.5 output:
##

Read 17463 atoms
Volume: 996.803 nm^3, corresponds to roughly 448500 electrons
No velocities found
    system size : 12.299  9.828  8.247 (nm)
    diameter    : 12.498               (nm)
    center      :  5.898  4.759  8.713 (nm)
    box vectors : 12.299  9.828  8.247 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 996.80               (nm^3)
    shift       :  3.852  4.991 -4.117 (nm)
new center      :  9.750  9.750  4.596 (nm)
new box vectors : 13.000 13.000 13.000 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1553.51               (nm^3)

## Last line of the output .gro file:
  13.00000  13.00000   9.19239   0.00000   0.00000   0.00000   0.00000
6.50000   6.50000

## g_mindist output:

Last frame          0 time    2.000

The shortest periodic distance is 2.59235 (nm) at time 2 (ps),
between atoms 3915 and 6814



Thanks in advance,
Thomas


On 26 April 2012 15:36, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hey Thomas,
>
> The rhombic dodecahedron corresponds to the packing of a sphere.
> Consequently, the difference in the distance between periodic images
> over the shortest diameter and the longest diameter is pretty small.
> That means that there isn't really an optimal orientation in a rhombic
> dodecahedron; all orientations are pretty much equal. And that's how
> it should be :)
>
> Cheers,
>
> Tsjerk
>
> On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis <tevang3 at gmail.com>
> wrote:
> > Dear GROMACS users,
> >
> > I have noticed that for constant box dimensions the minimum distance from
> > the periodic images of a protein depends on the initial orientation of
> the
> > protein, whereas the orientation of the dodecahedron relative to the
> x,y,z
> > axes remains fixed. These are the command lines I use:
> >
> > pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff
> > amber99sb-ildn -water tip3p -ignh
> > # set the new dodecahedron box dimensions
> > editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o
> protein_box.gro
> > # solvate with TIP3P
> > genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro
> -p
> > protein.top
> > # add ions
> > grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o
> > protein_ions.tpr
> > echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p
> protein.top
> > -pname NA -nname CL -np 3
> >
> > grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o
> > protein_EM.tpr
> > mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM
> >
> > # to see a dodecahedron
> > echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s
> > protein_EM.tpr -o em_dodecahedron.xtc
> > # measure the minimum distance from the periodic images
> > echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi
> >
> >
> > Is there any way to optimize the orientation of protein inside the
> > dodecahedron in order to get the maximum possible mindist?
> >
> >
> > Thanks in advance,
> > Thomas
> >
>
>
-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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