Hi James, thanks for reporting this. We sent you an email to determine the issue.

Okay, Thanks.

The error message ("atom N not found in buiding block 1ACE while combining tdb and rtp") suggests that, in your model, 1ACE contains a N that should not be there (according to GROMACS topologies). You might have to remove it, or move it to the next residue. You can reorganize atoms, residues, etc. easilyby just dragging nodes around in the Document View.

Hello, could you please tell us which graphics card you have? This seems to indicate a GPU issue.

Indeed in the current version of the Gromacs Wizard, you will need to have a force field which allows for both biomolecules and CNTs. Then you can add such a force field in the settings of the module. However using a 'one-shot parameterization' (e.g. using the ATB server) will not work at the moment with the Gromacs Wizard.

@dmitriymarin @admin It actually was this. Thanks for solving the problem!

Thank you, Stephan. I will give it a try.

Dear @dmitriymarin thank you very much. It works.

Thank you @Emmanuel for reporting these issues. We have fixed them - the Elements will be updated automatically once you launch SAMSON.

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.

Thanks for reporting this bug! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed this monday (may 11, 2020).

Thanks Dear.

Hello Arturo,

thanks for your interest in SAMSON!
The AutoDock Vina element has been deprecated as it was offering limited functionality (only one ligand at a time). It is still possible to use the AutoDock Vina Extended element for free for 30 days (no credit card needed) and it can do more, including pre-minimization of ligands and docking entire libraries.
Can you please ask your teacher to contact us at contact@samson-connect.net so we can find the best solution to provide access to all students?

Thanks,
Stephane

Adenita needs older versions of SAMSON because it hasn’t been updated yet (you can see this on the element page). You need to reinstall SAMSON and check the box “Install older versions” to install 0.8.5. Also, please check the requirements on the element page.

Currently, it is not possible because the selection filter functionality is not exposed to external elements. We will update it in the upcoming release of SAMSON.

@emmanuel
For now, you can just reapply the Hydrophobicity color scheme (Biology menu > Colorize > Hydrophobicity).

Dear @Oliver ,

We expect it to be fixed in a few weeks.

Dear @charlie,

For now, Adenita is provided only for SAMSON with version not higher than 0.8.5, (see Latest versions section on the module's web-page). So, to use Adenita you will need to install SAMSON 0.8.5.

You can request the newer version from the Adenita developer ( @Elisa ) here: https://forum.samson-connect.net/topic/139/user-support-adenita .

Yes, I could already run it.
Thank you!