When trying to visualize NBO on Gauss View, you might encounter an unexpected trouble that the orbital number of log file does not match the number on Gauss View.
This happens since NBO calculation automatically reorder orbital numbers.
In the end of the log file, reordering numbers were listed, however many people do not realize it…..
This article explains how to visualize the NBO on Gauss View!
<注> 日本語版はこちらNBO 計算結果の可視化方法！
preparation of input file
Please use the following keyword “pop=(NBOread, saveNBOs) ”
Also add the following two lines after the coordinates.
Numbering of orbitals
As we mentioned just before, NBO calculation reorders the orbital numbers.
The correspondence table of the orbital number is written at the end of the log file. Please search by “Reordering of NBOs for storage“. Then, table of numbers shown below will come out.
As seen from this table, the numbers indicate the orbital number “in the log file“, and the position of each number indicates the number “on Gauss View“. The position numbers are numbered 1, 2, 3 … in order from the left. There are 10 numbers in one row.
For example examples, in the above picture, orbital number 67 in the log file corresponds to orbital number 1 on Gauss View.
Similarly, orbital number 77 in the log file corresponds to orbital number 10 on Gauss View. Orbital number 3 in log file corresponds to orbital number 43 on Gauss View.
A Program for Orbital Number
If you manually find the corresponding orbital numbers, you would make mistakes. Therefore, we wrote a program for it.
Please download the program from the link below.
This program is written in C++. In order to use this program, please compile and execute this program using the following commands.
g++ NBO_analysis.cpp -o NBO_analysis
When you start this program, you will first be asked for a threshold value for displaying the interactions. Normally you should choose a value of 10 or more. Interactions less than 10 kcal/mol often do not contribute much.
For example, if threshold is set to 10, all interactions above 10 kcal / mol will be displayed. Enter “y”, “YES” or “Yes” if you are OK with this, otherwise enter “n”. If you want to display more or fewer interactions, then enter higher or lower threshold, respectively.
If you enter “yes”, then move to next step: finding the corresponding orbital numbers.
Here, please enter the orbital numbers based on the results shown just before. In this example, the strongest interaction is 355.68 kcal/mol. This interaction is between orbital 89 and orbital 90.
So, let’s focus on orbital 90. Please enter 90.
According to this program, orbital 90 in the log file is orbital 94 on Gauss View!
When terminate this program, please enter 0.
How to visualize on Gauss View
Next, let’s visualize the orbital on Gauss View! Please open the chk file on Gauss View. Then, select “Tools > MOs”.
The orbitals are displayed on the right side as shown below. So, please select 94 and make it yellow. Then click visualize!
As shown above, the orbital is visualized. According to the log file, this orbital corresponds the N–H bond, which is much with the picture above!
If you find any mistakes or have questions, please email us.
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