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.
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.
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 firstname.lastname@example.org so we can find the best solution to provide access to all students?
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.