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

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 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

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.

Hi Eva, maybe you can also try the Protein Path Finder (PPF), which gives you more control about the motion. E.g. here's a quick test below where I "unfolded" 1YRF using the Twister editor, with one part essentially not moving. Then I used UFF and FIRE as parameters in the path search, and two control points (one in the static part, and one in the mobile part). Note that the path can then be smoothed by the P-NEB module.

Hello,

The issue is that SAMSON was installed as Administor. Can you please try to activate User Access Control (UAC) so that Windows does not install SAMSON as admin? Here's a link about how to do that: https://www.technipages.com/windows-enable-disable-user-account-control-uac

Please set UAC to e.g. "Always notify" (you can set it back to the previous setting afterwards).

Then, please restart your computer, and install SAMSON again.

Please let me know how this goes.

Thanks,

Stephane

Awesome, you're welcome! Happy designing!