VMD-L Mailing List

From: Ari Turpeinen (ari.turpeinen_at_oulu.fi)
Date: Tue Sep 24 2013 - 03:23:51 CDT

On Tue, Sep 24, 2013 at 10:37 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Sep 24, 2013 at 8:20 AM, Ari Turpeinen <Ari.Turpeinen_at_oulu.fi>
> wrote:
> > Hi all,
> >
> > The cubegen utility included with Gaussian 09 rev D.01 creates cubefiles
> > that do not seem to be compatible with the cubeplugin in VMD 1.9.1
> > (LINUXAMD64 version). Cubes generated with rev C.01 work perfectly.
> >
> > I ran into the problem when trying to visualize electrostatic potential
> maps
> > by following the steps in
> > http://www.chem.gla.ac.uk/staff/granth/esp-map.html Opening the density
> cube
> > results in the following console output (similar for the esp cube):
> >
> > Console output (cube generated w/ rev D.01 cubegen)
> > ====================================================
> > cubeplugin) Coordinates will be rotated to comply
> > cubeplugin) with VMD's conventions for periodic display.
> > cubeplugin) Calculation of unit cell size failed. Continuing anyways...
> > cubeplugin) Coordinates will be rotated to comply
> > cubeplugin) with VMD's conventions for periodic display.
> > cubeplugin) Calculation of unit cell size failed. Continuing anyways...
> > Info) Using plugin cube for structure file
> > /home/ariturpe/Desktop/cubet/g09D_dens.cube
> > cubeplugin) trying to read cube data set 0
> > Info) Analyzing Volume...
> > Info) Grid size: 1x0x0 (0 MB)
> > Info) Total voxels: 0
> > Info) Min: 0.000000 Max: 0.000000 Range: 0.000000
> > Info) Computing volume gradient map for smooth shading
> > Info) Added volume data, name=g09D_dens.cube : Gaussian Cube: cb7_new
> > density
> > Info) Using plugin cube for coordinates from file
> > /home/ariturpe/Desktop/cubet/g09D_dens.cube
> > Info) Determining bond structure from distance search ...
> > Info) Analyzing structure ...
> > Info) Atoms: 126
> > Info) Bonds: 147
> > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 1
> > Info) Waters: 0
> > Info) Segments: 1
> > Info) Fragments: 1 Protein: 28 Nucleic: 0
> > Info) Finished with coordinate file
> > /home/ariturpe/Desktop/cubet/g09D_dens.cube.
> > ====================================================
> >
> > For comparison, output from cube file generated with rev C.01 cubegen
> > ====================================================
> > Info) Using plugin cube for structure file
> > /home/ariturpe/Desktop/cubet/g09C_dens.cube
> > cubeplugin) trying to read cube data set 0
> > Info) Analyzing Volume...
> > Info) Grid size: 95x93x58 (7 MB)
> > Info) Total voxels: 512430
> > Info) Min: -0.000000 Max: 3.158510 Range: 3.158510
> > Info) Computing volume gradient map for smooth shading
> > Info) Added volume data, name=g09C_dens.cube : Gaussian Cube: cb7_new
> > density
> > Info) Using plugin cube for coordinates from file
> > /home/ariturpe/Desktop/cubet/g09C_dens.cube
> > Info) Determining bond structure from distance search ...
> > Info) Analyzing structure ...
> > Info) Atoms: 126
> > Info) Bonds: 147
> > Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 1
> > Info) Waters: 0
> > Info) Segments: 1
> > Info) Fragments: 1 Protein: 28 Nucleic: 0
> > Info) Finished with coordinate file
> > /home/ariturpe/Desktop/cubet/g09C_dens.cube.
> > ====================================================
> >
> > The differences between the cubefiles generated by different cubegen
> > versions are too large to be included here, but I can provide the
> cubefiles
> > if there is interest.
>
> there is obviously a difference in the header segment of the cube
> files that throws the parser off. can you just post the first 10 or so
> lines from both of your files?
>
Thank you for the quick response. There's an added 1 in the fifth column on
the third row.

ariturpe_at_spin:~/Desktop/cubet$ head -n 10 g09C_dens.cube
 cb7_new density
 Electron density from Total SCF Density
  126 -17.756981 -17.182058 -10.717971
   95 0.376223 0.000000 0.000000
   93 0.000000 0.376223 0.000000
   58 0.000000 0.000000 0.376223
    8 8.000000 -7.276515 -0.161584 5.411098
    8 8.000000 -5.021790 -6.490272 5.802173
    8 8.000000 1.884070 -8.013025 5.773882
    8 8.000000 7.197353 -3.577459 5.716781
ariturpe_at_spin:~/Desktop/cubet$ head -n 10 g09D_dens.cube
 cb7_new density
 Electron density from Total SCF Density
  126 -17.756981 -17.182058 -10.717971 1
   95 0.376223 0.000000 0.000000
   93 0.000000 0.376223 0.000000
   58 0.000000 0.000000 0.376223
    8 8.000000 -7.276515 -0.161584 5.411098
    8 8.000000 -5.021790 -6.490272 5.802173
    8 8.000000 1.884070 -8.013025 5.773882
    8 8.000000 7.197353 -3.577459 5.716781

-Ari

> The release notes for Gaussian 09 rev D.01 contain the following regarding
> > cubegen: "The cubegen utility now correctly produces Laplacian and ROHF
> > density. It also now correctly computes the current density from jobs
> with
> > basis sets with pure functions (5d 7f)." (In section bugfixes between G09
> > revisions D.01 and C.01)
>
> this is irrelevant, but in the process some change in the file format
> seems to have slipped in as well.
>
> axel.
>
>
> >
> > -Ari
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>