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:

Please see the gif attached:

@humera said in Ligand Receptor Interaction:

One more thing is that when I expand selection to 'side chains' within 6 angstrom of selected ligand, and then apply Licorice visual model. It displays few atoms as well along with side chains.
In short I want to display the side chains which are interacting with ligand, or which act as a binding site.

To select side chains around a ligand:

• Select a ligand
• Biology menu > Binding sites: Select Use the current selection as ligands in the Ligands box and Side chains in the Binding sites box, and specify the distance from ligands.

To visualize them using the Licorice visual model: Visualization menu > Licorice (Ctrl+Shift+V). But I would recommend visualizing the whole residues with the licorice visual model. If you don't want to see atoms, you will need to hide them: uncheck nodes in the Document view which you want to hide.

Dear @HUMERA ,

To visualize hydrogen bonds you can use the Hydrogen Bond Finder element - just click Add and it will appear in you SAMSON installation next time you launch SAMSON.

Dear @HUMERA ,

Thank you for your feedback. Could you please tell us what OS you are using?

Whenever I try to export image in the specified directory. It shows button as 'OPEN' instead of 'SAVE'. Moreover it DOES NOT save file. Check out this functionality.

The export of an image works, you need to specify the extension as well, e.g. image.png. Without the provided extension, it doesn't save - this will be fixed in the next version. The fact that the button says Open instead of Save is due to general file dialogs in SAMSON.

Moreover AutoDock Vina results file should contain separate columns for Score, RMSD etc..

If you click Export results in csv file under the results table, the csv file will contain separate columns with the Vina score (affinity) and rmsd (lower and upper bounds). To verify, you can open the saved csv file in a text editor.