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.

@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 Sebastian,

one possibility might be to ask the Vina extension to compute many modes (e.g. 1000) and then use a script to filter out the conformations that do not satisfy the distance constraint. Another possibility might be to directly modify the source code of Vina to add a term to the scoring function that would penalize one or more unsatisfied constraint(s) (similar to a NMR energy function). We're going to look into this. Thanks for the suggestion.

Best,

Stephane

@shozeb Here is the process to uninstall SAMSON :

delete : rm -rf ~/.local/share/OneAngstrom/
delete : rm -rf ~/OneAngstrom/
delete : rm -rf ~/Documents/OneAngstrom/
delete : rm -rf ~/.config/OneAngstrom/
delete : rm -rf ~/.config/NANO-D (if exists)

After that you may try to reinstall SAMSON as described in the documentation.

Don't hesitate to contact us again if the issue is not solved. Users are our priority.

Jocelyn

Dear @Ricardo-2 ,

Due to policy updates, we no longer support older versions of SAMSON and have removed them from access.
Could you please tell us which features are missing for you in the latest SAMSON and which version of SAMSON you want to install?

Ah ok good. Yes SAMSON determines which importer to use based on the file extension.

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.

Thanks!! Solved!

Dear @Tom-1 ,

We have added an example of how to build molecules using Python Scripting in SAMSON, please see SAMSON-Python-Samples > building.

Please let us know if you have any questions or feedback.

Hi Stephane,

thanks for your answer, I'll do that then.

Best

Laëtitia

Dear Stephane,

Thanks for the quick reply. I will add the position in three attributes for now. Looking forward to 0.8.0!

It seems it works. Thanks.

Perfect thanks.

Dear Camps,

I thought I'd clarify what's going on with Brenner and ASED-MO. While SAMSON and numerous SAMSON Elements are and will remain free forever, both for academia and industry, some SAMSON Elements will now have a commercial license (for industry and / or academia).

In effect, SAMSON Connect is becoming a marketplace for molecular modeling, where developers have the possibility to integrate and commercialize their tools (think App store for molecular modeling, except everything is integrated into a single, universal platform which makes it possible to combine modules together and gives new possibilities). Our goal is to contribute to the development of an integrated ecosystem for molecular modeling, where users can install tools in a few clicks, have them all integrated in the same platform, are able to combine them, pipeline them, etc. Since SAMSON has an open architecture, and the SAMSON API makes it possible for anyone to integrate existing tools, create new ones from scratch, develop new force fields, create new visualizations, etc., you can imagine the huge possibilities the SAMSON model gives.

As with other marketplaces (iOS, Android, etc.), many SAMSON Elements are and will continue to be free, and new free SAMSON Elements will continue to be published. However, our goal with this hybrid economic model is to reach the best of both worlds: serve the molecular modeling community while supporting the development of the best possible platform.

At the moment, anyone can get a free month of some commercial SAMSON Elements (including Brenner) by answering the short survey at https://forms.office.com/Pages/ResponsePage.aspx?id=Cg7MSY8KzkinPF492orBMZM0kpSnVmtKp3madpYYjexUQ0c5V1Q3VUEwVEtHQlhSWVVJRUFGN1lVQy4u.

At the end of the survey, they can choose which SAMSON Element they want among:

Brenner interaction model (interactive simulation for carbon nanotubes, graphene, etc.) Crystal creator (build complex crystals structures) Normal modes advanced (non-linear normal modes analysis for proteins binding sites)

and we'll add it to their account (registering is and will always be free, and SAMSON itself will always be free).

Best,

Stephane

Sorry for the issue!

I created a ticket.
thanks for your answer!

Thank you!
I will try it with this.

Yes, I meant SBStructuralGroup :)

Thank you! Using the GetClass and GetElementUUID methods is enough for my purposes :)

Thanks Ibrahima! Let us know if we can help in any way.