OneAngstrom

Ok thanks. I'm going to contact you by email for further exchange.

Could you please tell me whether you added custom force fields? (Using the + sign). If yes, please try to remove them (using the X sign) and try again, and let me know.
Thanks,
Stephane

Dear Guy,

thank you for your interest in SAMSON and the GROMACS Wizard extension. Could you please tell me whether you clicked "Compute fitted box" first, to indicate what system you want to simulate? It looks like nothing was selected, and no atoms were exported. I just did a quick test with 1AKI (the PDB indicated in the tutorial):

• removed the waters using the document view
• clicked Compute fitted box
• increased the box size to 7,015nm
• checked Add solvent and Neutralize system (using Ca and Cl)
• clicked Prepare

Here is what I obtain: (I added a secondary structure in the Biology menu)

If you'd like, you can use the 1AKI tutorial adapted for the GROMACS Wizard: https://documentation.samson-connect.net/gromacs-wizard/. Please let us know if you have any questions.

thanks,
best,

Stephane

@martin-1

Dear Martin,

Thanks for your feedback. It appears you’re on a very specific machine as most users install SAMSON within minutes without any issues on Windows Linux or Mac in standard directories. Please contact the developers at contact@samson-connect.net as indicated in the automated email you received about installation.

We’re happy you think SAMSON is looking good too :).

Best

Hello, high-resolution displays are not supported natively yet, but Windows 10 indeed allows you to change the settings. On my 4K monitor, I use the method explained there : https://blog.pauby.com/post/high-dpi-settings-windows-10/ , but I choose "System" instead of "Application". My system DPI adjustment is at 200% in Windows, and here is how it looks like:

Could you please let me know if this works for you?

Dear @Olivia ,

The Adenita extension has been developed and is supported by external developers ( @Elisa ). And Adenita is in an alpha stage and might have some issues. We plan on porting this extension to the most recent SAMSON version.

You can also copy your question to the specific topic: Adenita - User Support.

Great! Thank you for your reply!

Dear @Olivia ,

Please note that the Adenita extension is not yet available in the latest version of SAMSON. To use Adenita, you will need thus to install an older version of SAMSON (for example 0.8.5 or 0.7.0).

If you don't see any apps in your SAMSON please check if you have an Internet connection.

In what version of SAMSON, you don't see apps and Adenita?

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

Dear @Sherif-0 ,
Can you please tell us what plots do you want to have?
Thank you