Hello,

Thanks for your interest in SAMSON! If you’re on Windows, you will need to install the latest runtime from Microsoft. They are available here: https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads.

You should install vc_redist.x64.exe available from that page.

Best regards,

Stephane

@carmine Thank you very much for your feedback!

We will add other box types in one of the next updates of the GROMACS Wizard.

Options provided in the Additional parameters have bigger priority then options specified in the GUI. It is true, it would be nice to highlight them in some way.

Dear Sudhir, calculation time depends on the exhaustiveness (the higher the slower, but the more exhaustive the search is), the number of rotatable bonds in the ligands (each rotatable bond adds a search dimension) and the number of cores on your computer (the module takes all cores minus one, so your computer remains responsive). This seems normal.

Hello Emmanuel! We were actually talking about you just a few hours ago because we saw your posts about your VR class! It's awesome!

You can actually already move molecules with one hand if you use the "Move" mode (which moves stuff) instead of the "Navigate" mode (which moves yourself).

We decided to use both hands for navigation because we wanted the user to be able to scale as well as rotate / translate the view (7 degrees of freedom), and our tests have shown that this is what is familiar to many people (who use two fingers for scaling on phones). Using both hands and spreading arms / bringing arms closer changes your scale relatively to the molecules. When you move both hands without changing the distance between them you can rotate, translate, etc. Changing the scale in an intuitive way was really important to us to address many different scales as in the virus demo. In the frame below, the user height is around 0.1 microns:

while in this frame (inside the virus) the user height is about 1 nanometer:

(sorry for the video compression blur).

To move molecules instead of yourself, you use the thumbpad in "Move mode" (the two other thumbpad modes are "Add" and "Erase"), and you choose the selection filter that corresponds to what you want to move. This way, you can move a molecule with a single hand (or two molecules with two hands).

For example, in the Selection menu, choose the selection filter called "Structural models" as in the figure below:

Depending on your structures, you might want to select other levels (e.g. molecules, chains, etc., or the default "atoms and bonds").

Then, using the thumbpad, you can rotate / translate when you press on the thumbpad. This is demonstrated e.g. in this video where the user manipulates two carbon nanotubes at the same time to stick them together during interactive simulation. Each hand independently moves each nanotube.
.

You can have different modes in each hand (e.g. Add on the left hand, Move on the right hand, etc.).

I hope this helps. I'll be happy to talk more about it, as well as about extensions and applications.

Best,

Stephane Redon

Hi Petr, thanks for the suggestion. We are thinking we might actually go the opposite route, i.e. hide these elements from My SAMSON / My Elements, so that they cannot be removed.

It is saying it as a problem. Backing up of file is working anymore. Rest of the log is normal but it got stuck at this point and then nothing works.

Hi Arnaud, thanks for your interest in SAMSON and sorry about this crash. We are not able to reproduce it here. Could you please try to remove the GROMACS element and add it again as follows:

Sign in on SAMSON Connect, you will arrive in My SAMSON / My Elements On the SAMSON Element called "GROMACS interaction models", you should see an "Installed" button. When you hover the mouse over it, the button turns to "Remove". Click on it. Restart SAMSON, this will uninstall the GROMACS element. Quit SAMSON. On SAMSON Connect, the button mentioned above should turn to "Add again" (this might take a minute). Click on it. It should turn to "Pending". Restart SAMSON, this will install the GROMACS element.

Please let me know if this helps. Academic accounts are the ones with academic email addresses. Is it possible for you to sign up with one?

@admin one pdb file having protein and ligand docked.

Thanks a lot. Now it is working in the advanced element of AutoDock (normal one I did not check)
Thank you

Dear Stephane,
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.

Hi Andrea, sorry for the delay. Typization is normally performed automatically (this is a benefit of this SAMSON Element, as described in the paper Artemova, S., Jaillet, L., & Redon, S. (2016). Automatic molecular structure perception for the universal force field. Journal of computational chemistry, 37(13), 1191-1205.). The typization functions are there when you know for sure that you would like to use a different typization, but even then you should refer to the original UFF paper to make sure this is what you want.

wonderful!
Thanks

Great! Diana, thank you very much for providing good descriptions of your problem and solution - it might help others experiencing the same problem.

Sorry for the issue. Yes, the Python version is important since the Python Scripting Element is linked to a particular version of the Python library.

Dear Dimitriy,
Thank you very much.

Best Regards,

Surendra

Sorry for the issue!

Thank you so much sir....It really helped.

Dear Patrice, yes, it is planned in a very near future, I didn't have time for the update yet...
Regards,
Sergei

Gaussian surfaces may be slow to recompute sometimes (e.g. for large molecules), so there is an "Update" button to recompute the surface. You need to use it when you change the color.

About the transparency: it depends on the order of visual models. Since order-independent transparency is not yet implemented, you will see the secondary structure only if it comes before the gaussian surface (when you traverse the document in depth-first order).

Here is an example with the Gaussian surface first:

And here is an example with the Gaussian surface after the secondary structure: