Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).

First, you will need to modify SAMSON preferences (Ctrl+K):
-1- For the Add editor, disable the "Adjust hydrogens ..." option.

-2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.

Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.

Dear @Kevin-3 ,

Thank you for posting this question here.

To create such a model you will need to have the Brenner interaction model. It is a paid element, but there is a free trial available and special prices for Academia.

You can check out the SAMSON Tutorials - Essentials 18 - Interactive simulation video that explains how to perform interactive simulations in SAMSON. This video is for an older version of SAMSON, but it should be helpful. To create a model that you attached you would need to create a graphene sheet and then place a nanotube of the desired radius perpendicular to it (you can move, rotate objects using Move editors in SAMSON) and connect them using the same approach as described in the video. So the pipeline would look like this:
-1- Add graphene sheet and nanotube. You can first add a nanotube using the Nanotube creator GUI - this will allow for precise positioning and size - and then placing a graphene sheet. You may also place them using Move editors in the arrangement close to the desired structure. You can use the Viewport compass to rotate the view by precisely 90 degrees and the Zoom to fit to center the model in the viewport (Ctrl+Shift+Space, Shift+Space).

-2- You can remove some atoms from the graphene sheet in the place of the desired connection to facilitate this connection in the following simulation step.

-3- Add a simulator (Ctrl+Shift+M, or Home > Add simulator). Set the Brenner interaction model as an interaction model, set Interaction modeling as a state updater. Increase the state updater's step size to e.g. 0.5 fs.

-4- Start the interactive simulation by clicking Space or Home > Start simulation.

-5- You can select the nanotube in the Document view and move it using Move editors closer to the graphene sheet for bonds to be automatically created between them thanks to the simulator. Else you might need to help to connect them by hand as shown in the video above using Select (shortcut: R) and Move atoms (shortcut: D) editors or Add editor (shortcut: A) (it's Carbon by default).

You can also check the SAMSON User guide - Modeling and Simulation on how to perform simulations in SAMSON.

Thank you!
This looks like an issue with some integrated graphics cards. We will look into how we can reproduce it and fix it.

Dear @Mizraim,

Could you please check what OpenGL version do you have installed? It should be higher than OpenGL 3.2.

Dear @Ben,

For simple minimization of protein-CNT, you can use Universal Force Field in SAMSON, but it will not be suitable for MD simulation. You can try using the Gromacs Wizard module for simulation of protein-CNT interactions. See e.g. this tutorial from Gromacs: Gromacs How-To: Carbon Nanotube. But it describes only CNT simulation. As for the simulation of protein-CNT interaction you might need to check which force field to use and maybe modify some FF parameters.

This is due to the special symbol ("é") in your path. Could you please rename the folder or put the files in a folder with the path that doesn't contain special symbols. We will try to fix this issue in the next version of SAMSON.

Thank you for reporting the problem!

Does the part of the protein that you want to be fixed stay at the same place in both conformations? Because, basically, the ARAP Interpolation Path Element produces an interpolated path between two conformations and if the parts that you want to be fixed are placed differently in the start and goal conformation then it will interpolated between those positions.

Do you have the Perform alignment before interpolation checked or unchecked? If checked, it will align the start conformation onto the goal conformation before performing ARAP interpolation.

You may also go in two steps by specifying the pivot conformation: 1) start -> pivot; 2) pivot -> goal. And then you can combine paths.

You can also try to use the Normal Modes Advanced Element to produce the movements of a protein from a single conformation.

@humera

I followed these steps but still certain atoms appear, and those atoms were hydrogen atoms. I resolved this issue by removing all hydrogen atoms from structure. But it is not a good solution since sometimes we have to display hydrogen atoms to indicate hydrogen bond.

The hydrogen atom might appear if, for example, you add them yourself using e.g. Add hydrogens. You don't need to delete atoms to hide them, you can just hide the structure in e.g. Document view (see the gif in the answer above). To learn more, I recommend you to go through interactive tutorials in SAMSON: Help > Tutorials.

@humera

Is there any SAMSON element available which can display cysteine disulphide bridges?

Cysteine disulfide bridges are displayed as bonds.
You cand find SS-bonds using e.g. Node Specification Language (NSL): S linking S (which stands for Sulfur atom linked to another Sulfur atom).
And to find precisely Cysteine disulfide bridges: (S in residue.type CYS) linking (S in residue.type CYS) (short version: (S in r.t CYS) l (S in r.t CYS)).

Dear @HUMERA ,

You can import .csv in Excel with any delimiter using Data > From Text/CSV and then select the delimiter: