Hello, here is a capped nanotube for SAMSON 0.7.0.
Hope this helps.
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.
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.
Hello, could you please try to add it in the Additional parameters section of the Simulate tab? (Under "Saving interval", you should see the "All..." push button.
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.
Unfortunately, SAMSON Elements cannot contain any GPL code. The reason is that SAMSON Elements are dynamically loaded at runtime and tightly integrated with SAMSON and with each other. According to the GPL FAQ (https://www.gnu.org/licenses/gpl-faq.en.html#GPLPlugins) :
If the main program dynamically links plug-ins, and they make function calls to each other and share data structures, we believe they form a single combined program, which must be treated as an extension of both the main program and the plug-ins. If the main program dynamically links plug-ins, but the communication between them is limited to invoking the ‘main’ function of the plug-in with some options and waiting for it to return, that is a borderline case.
Since SAMSON is not open source (we believe developers of SAMSON and SAMSON Elements should be free to choose whether they distribute their source or not), GPL code cannot be used in SAMSON Elements (and is not used in SAMSON either).
If you want to distribute your source code (as we do for some of our own SAMSON Elements and tutorials: https://github.com/1A-OneAngstrom), you should choose a license that is compatible with this hybrid approach (i.e. mixing closed and open source). This includes Apache, MIT, LGPL, and BSD for example. For our open source code, we have used BSD-3.
Note that it is possible to write SAMSON Elements that perform calls to external executables, even if these external executables are based on GPL code. However, these GPL-based external executables should be installed separately by users.
I hope this clarifies things,
Hi Elisa,starting with 0.7.0, the Element Generator is now a SAMSON Element that you can find at https://samson-connect.net/app/main?key=element&uuid=b0d9900c-b058-e7fa-4c31-d85f18b9c4e2.
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