VMD-L Mailing List

From: Ari Turpeinen (Ari.Turpeinen_at_oulu.fi)
Date: Tue Sep 24 2013 - 01:20:18 CDT

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.

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)

-Ari