Hi,
I want to make an input file for using ONIOM method in Gaussian. System contains nanotube functionalized(by amino acid) interacting with a complex protein. when i want to build 3 layer for different(low, mwdium and high) levels, it's really hard to choose part of protein,... for high level. Is there any easier and reliable way to make correct input for this objective?
Regards
When you opened the structure in Gaussianview, you can divide different layers in Tools/Atom Group, and then select "ONIOM Layer" in Atom Group Class selection, and thus you can define the high or low layer by atom label. The other way, you can define the different layers in Tools/Select Layer by click atoms.
You can define your layers using:
GaussView/Tools/ Select layer
GaussView/Tools/ Atom list
You can control your layer selection using :
GaussView/Tools/ Atom groups/ ONIOM layer (High light layers)
Hi Roja,
Pull up or make the image(s) of what you want to treat with ONIOM. Then look at your tool bar in Gaussview and find the icon with 3 colored layers. You will see a window “Layer Selection Tool”. The Set Layer: should be set on Low. I just click on Select All at this point. All of the atoms will turn a light blue. Now click on Apply and every thing turns into a wire model. Now go up to the pull down menu that says Low and change that to High (or Medium if you want). Click on one of the atoms that you want to be in the High layer and the bonds leading to it will again turn light blue. Here’s where you get to play with the Expand Selection slide bar to turn those bonds (and atoms) to the High layer. Now! Once you have selected your atoms/bonds for the High layer, make sure you click on the Apply button again. The High layer atoms and bonds will change to the usual Gaussview model, so that you can see which atoms/bonds are in which layer. When you are finished, click on the Close button. When you go to your Gaussian Calculation Setup window and get to the Method tab – make sure you click on the Multilayer ONIOM Model button in the upper right hand corner and another window will open that has three tabs High Layer, Medium Layer and Low Layer. Pick your Method: , Basis Set: and Charge: like you usually do, but do it for each layer. Go onto the other tabs as you normally do and you will see that the job should launch with your desired calculation setup. It took me a while to figure this out step by step without missing an important detail, so I hope this will answer your question.
---Shannon
Thank you so much dear shanon for your detailed answer. It was really helpful.
Best
Roja
- Badges
- Science topic