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Error for Gaussian16 .log files and GaussView5


There’s an error message when opening some Gaussian16 output files in GaussView5 for which the message displayed is the following:

ConnectionGLOG::Parse_Gauss_Coord(). 
Failure reading oriented atomic coordinates. Line Number

We have shared some solutions to the GaussView handling of *chk and *.fchk files in teh past but never for *.log files, and this time Dr. Davor Šakić from the University of Zagreb in Croatia has brought to my attention a fix for this error. If “Dipole orientation” with subsequent orientation is removed, the file becomes again readable by GaussView5.

Here you can download a script to fix the file without any hassle. The usage from the command line is simply:

˜$ chmod 777 Fg16TOgv5
˜$ ./Fg16TOgv5 name.log

The first line is to change and grant all permissions to the script (use at your discretion/own risk), which in turn will take the output file name.log and yield two more files: gv5_name.log and and name.arch; the latter archive allows for easy generation of SI files while the former is formatted for GaussView5.x.

Thanks to Dr. Šakić for his script and insight, we hope you find it useful and if indeed you do please credit him whenever its due, also, if you find this or other posts in the blog useful, please let us know by sharing, staring and commenting in all of them, your feedback is incredibly helpful in justifying to my bosses the time I spent curating this blog.

Thanks for reading.

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fchk file errors (Gaussian) Missing or bad Data: RBond


We’ve covered some common errors when dealing with formatted checkpoint files (*.fchk) generated from Gaussian, specially when analyzed with the associated GaussView program. (see here and here for previous posts on the matter.)

Prof. Neal Zondlo from the University of Delaware kindly shared this solution with us when the following message shows up:

CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Rbond
Line Number 1234

The Rbond label has to do with the connectivity displayed by the visualizer and can be overridden by close examination of the input file. In the example provided by Prof. Zondlo he found the following line in the connectivity matrix of the input file:

2 9 0.0

which indicates a zero bond order between atoms 2 and 9, possibly due to their proximity. He changed the line to simply

2

So editing the connectivity of your atoms in the input can help preventing the Rbond message.

I hope this helps someone else.

Efficient use of the clipboard on GaussView


Editing large molecules on a seemingly simple visualizer as GaussView can be a bit daunting. I’m working on a follow up of that project we recently published in JACS but now we require to attach two macrocycles to the organometallic moiety; the only caveat is that this time we don’t have any crystallographic data with which to start. Generating a 3D model of this structure is already hard enough and even when you managed to do it there are many degrees of freedom that in some cases can lead to unrealistic geometries after optimization.

I recently came across a simple way to edit a large complicated molecule by optimizing the fragments separately and then joining them in a new molecule by using the clipboard. This rather simple method, that I for one had never exploited has just saved me a few good hours.

Copy a molecule (CTRL+C) and it will go to the clipboard as a molecular fragment for which you can define a new hot atom and thus bind it to the other fragment as you would with the regular builder. I strongly suggest to use a “New Molecule Group” instead of editing over an existing molecule. Also, if you are using the “paste” button, observe that it has three different options; you may want to use the last one “append to existing molecule” or you will have your fragments in different windows.

And remember, dihedral angles are your best friends.

Some .fchk files wont open in GaussView5.0 (Update)


A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.

CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Orbital Energies
Line Number 1234

Although the method described in the previous post works just fine, the following update is a better approach. Due to a change of spelling between G03 and G09 (which has been corrected for G09 but not available for GV versions prior to 5.0.9) one must change “independent” for “independant

To make the change directly from the terminal the following command is needed:

sed -i 's/independent/independant/g' file.fchk

Alternatively you can redirect the output to a new file

sed -e 's/independent/independant/g' file.fchk > newfile.fchk

if you want to keep the old version and work with a new one.

Of course this edition can be performed manually with any text editor available (for example if you work in Windows) but solutions from the terminal always seem easier and a lot more fun to me.

Thanks to Dr. Fernando Cortés for sharing his insight into this issue.

If a .fchk file wont open in GaussView5.0


I’ve found the following error regarding the opening of .fchk files in GaussView5.0.

CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Orbital Energies
Line Number 1234

The error is prevented to a first approximation (i.e. it at least will allow GV to open and visualize the file but other issues may arise) by opening the file and modifying the number of basis functions to equal the number of independent functions (which is lower)

FILE HEADER 
FOpt RM062X 6-311++G(d,p) 
Number of atoms I 75
Info1-9 I N= 9
 163 163 0 0 0 110
 2 18 -502
Charge I 0
Multiplicity I 1
Number of electrons I 314
Number of alpha electrons I 157
Number of beta electrons I 157
Number of basis functions I 1199
Number of independent functions I 1199
Number of point charges in /Mol/ I 0
Number of translation vectors I 0
Atomic numbers I N= 75
... ...
... ...

Once both numbers match you can open the file normally and work with it. My guess is this will continue to happen with highly polarized basis sets but I need to run some tests.

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