Visualizing Gaussian ONIOM inputs with VMD

This python script converts Gaussian *.com or *.gjf inputs to a PDB file. All ONIOM and frozen layer details are added to the PDB chain and segid columns. This can be later used to create atom selections in VMD.

Installation

Download all files manually or clone the repository using:

git clone git@github.com:madhurangar/oniom-vmd-visualisation.git

Usage

Execute the python script with correct system arguments:

python3 path/to/gau2pdb.py input.gjf output.pdb

for help and to see commandline options, try python3 path/to/gau2pdb.py -h

Example

All files are tutorial located at tests folder. First, do the file conversion.

python3 ../gau2pdb.py case2.gjf case2.pdb

Then open the PDB in VMD (vmd case2.pdb) and carry out the visualisation. Now you can see all ONIOM and frozen layer information in atom selection options.

# file: vmd-styles.tcl
display nearclip set 0.010000
display projection Orthographic
color Display Background white
display depthcue off
color Axes Labels black

mol modselect 0 0 chain H
mol modstyle 0 0 CPK 1.000000 0.400000 120.000000 12.000000
mol modmaterial 0 0 AOEdgy

mol color Name
mol representation Licorice 0.100000 120.000000 12.000000
mol selection chain L
mol material AOEdgy
mol addrep 0

Finally, render your visualisation.

render Tachyon vmdscene.dat "path/to/vmd" -aasamples 12 %s -format TARGA -res 1024 1024 -o %s.tga

Enjoy!