Some software trickery…

This post will become updated continuously in order to include as much of these useful tips as I find along the way, so if you are interested please subscribe so you don’t have to visit often. Some are old or even a bit obsolete in terms of software versions but I still include them so they can all be gathered in one place; this is basically a summary of some common errors in the use of Gaussian (G03 and G09). Please feel free to comment on this post, sharing your tricks with various programs in whatever branch of computational chemistry you might be working on.

Vibrations calculated with Gaussian 09 can’t be visualized with GaussView 3.x

*Change the lines “Atom  AN” with “Atom AN”. They look the same but there are TWO spaces in the first (this is the way G09 prints the output files) and in the second one there is only ONE space. The credit is entirely due to Jean Poully who posted this trick on the CCL a few months ago.

*Reader John Keller from Alaska suggests to use the formatted chk file (.fchk) to avoid this problem. As usual with formatted chk files make sure you format them in the same computer where you calculated it, or at least make sure both versions are compiled under the same architecture (32 or 64 bits).

Molecules appear flat on Molekel versions previous to 5.x

Molekel 4.x reads Gaussian98 files only. Gaussian03 and Gaussian09 files need to have the header corrected in the following part, right at the beginning of the file:

Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009

Change to:

Gaussian 98:  EM64L-G09RevA.02 11-Jun-2009

A rather old one and kind of a weird one too but it works and some of us (myself very much included) like the previous Molekel far more than the new 5.x version.

Electrostatic potentials can not be visualized with Molekel 4.x

This is an error that stems from the fact that atomic charges are not read by Molekel, so all electrostatic properties derived from them are not calculated nor visualized. The problem is that Gaussian also changed the header for the charges when going from Gaussian98 to Gaussian03. In Gaussian 98 charges are labeled as “Total Atomic Charges”. In G03 and G09, atomic charges are labeled “Mulliken Atomic Charges”. Therefore find and change this label for the latter. PLEASE NOTE that Molekel will look for the title “Total Atomic Charges” so if your calculation was a geometry optimization then you have to find the set of charges that correspond to the last step of it. Look for the last string and change that one; you may also change them all with the right edition option in your editor, Molekel will use the last one since that should be the one corresponding to the optimized structure.


I’ll post something else when I find/remember it. Thanks for reading!

Mi amor!!!
Muchísimas felicidades!!! Estoy muy orgulloso de ti, de ser tu novio y tenerte en mi vida. Como persona y como profesional no eres más que admirable. Al igual que quienes te escriben, estoy seguro que este es solo el principio, mi amor, ese negocio en tus manos va a llegar hasta donde tu papá siempre quiso y aun más lejos. Te amo y estoy

About joaquinbarroso

Computational and theoretical chemist in his early forties, in love with life, science, baseball, and literature. Science literacy makes us responsible citizens, it is therefore a scientific duty to talk, write, and engage with the general public; as Feynman said, if you find science boring, your learning from the wrong teacher. "Make like a molecule and react!"

Posted on August 3, 2010, in Computational Chemistry, Gaussian, Software, Tricks and tagged , , , . Bookmark the permalink. 4 Comments.

  1. Motowo Yamaguchi


    I have a problem to display the spin density calculated by Gaussian03 using Molekel 4.3. It was possible to calculate and display “spin on atom” for the calculation of the anion radical, but the trial of “spin density” gave the error message: “Marching Cubes: cutoff above maximal value”.
    I should be very grateful if you would kindly give me any advise.

    P.S. I could display both SOMO and HOMO orbitals of the anion radical.

    • Hi Motowo!

      I could have sworn I had already replied to this comment. Well, never mind!
      Try generating individual cube files in your gaussian calculation and then load them individually to molekel4.3.
      Let me know if this helps because I’m not sure about it, I haven’t had that problem before so if you let me know more about it we may help others with the same issue.

      Thanks for reading!

    • Hello! I have met the same problem with you, could you tell me how did you solve this problem of Molekel 4.3? Thank you very much!

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