Currently, there is no public extension in SAMSON that can launch/use LAMMPS. But you can export your system into a LAMMPS Data format and load LAMMPS files (data and trajectories) back in SAMSON.

We plan on adding the support for periodic boundary conditions in one of the future releases of SAMSON. For some systems, you can simulate without PBC or by freezing the boundary atoms to fix them.

You can also combine simulations in SAMSON with e.g. ASE package using Python, see Python scripting: Combining SAMSON simulation with ASE calculators

Dear @David-Adrian ,

Thank you for your feedback! We will consider this for future releases. Where would you like to install it, e.g. on another drive or a USB-stick?

Dear @Mattia-Felice ,

Thank you for the feedback! We will consider this for the next releases of SAMSON.

We will surely add more labeling possibilities in the next release.

As for formats from ab initio packages, SAMSON currently supports only Molden and it loads only the molecular structure from it. But we can add the possibility to load other data from it as well.

Dear Rudy, sorry for the delay. You can simply merge the ligand structure into the receptor structure. Precisely, in the document view, drag the ligand node and drop it onto the receptor node (more generally, you can drag and drop nodes around to reorganize your entries).

Then, when you select the receptor and compute the normal modes, the ligand will be taken into account.

Dear @Serena ,
No, we do not use Open Babel or anything else for that. It is done by the AutoDock Vina Extended module.

Dear @AntiDown ,

Ok. I am glad it works for you now.
Thank you for your reply!

Great! I am glad that it worked!
Do not hesitate to contact us if you have any questions or feedback.

Great! Thanks for letting us know.

Hi Pedro,

We're sorry about the issue.

Could you please try to delete the following folders:

(IMPORTANT: make sure you don't have e.g. personal SAMSON documents in these folders that you might want to preserve.)

C:/Users/[USERNAME]/AppData/Local/OneAngstrom/
C:/Users/[USERNAME]/OneAngstrom/
C:/Users/[USERNAME]/Documents/OneAngstrom/

and try to reinstall SAMSON to see what happens?

Maybe there is a need to specify in your Windows settings that SAMSON should use specifically the NVIDIA GPU ? Please let us know.

Dear @Filipe

Normally it should be rendering double bonds by default, but you can change this setting in Preferences > Rendering > Structural models - check the Render multiple bonds option:
5d539e47-b05e-4872-8cc1-d1d36cb34dc5-image.png

As for the PBT format, currently, SAMSON does not have the PBT format exporter, but you can export in OBJ or glTF formats for use in Blender.

Best,
The SAMSON Team

Great contribution!

Hi @albert ,

There are several options for the colorization of structures or visual models (Ribbons is a visual model) based on chains:

The colorization using color schemes. First, select the Ribbons visual model in the Document view that you would like to colorize. Then: Biology > Colorize > Chain ID or Chain (illustrative) (i.e. in the style of D.S.Goodsell)
aedf2d1e-77e3-42cd-af72-51400ba6f73b-image.png
You can also choose "Custom..." from the list and specify the color palette. The colorization with constant colors per chain. Choose a chain in the Document view. Set the color using Visualization > Colorize.

See more in User guide - Colorizing and User guide - Visualizing.

Dear @Zilong

It’s not currently possible to export vector images. However, you can change the image resolution in the preferences:

Open the Preferences (Menu Interface > Preferences) In the Preferences, go to Interface > Captures to change capture settings, including the resolution.

Great! Thanks Tom!

Thanks Tom!

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.

Dear @闽乐 ,

In the new version, you can access the control parameters for the visual model via the Inspector. For that, simply select the Adenita visual model and open the Inspector - you can right-click on the Adenita visual model and choose Inspect in the context menu.

See: User guide - Inspecting

Dear @Elsaid ,

This happens because of the Wayland display server on Ubuntu. You can try specifying another display server.

If you launch SAMSON from a terminal, then you could first specify the environment variable QT_QPA_PLATFORM to use the Xorg display server (X11):
export QT_QPA_PLATFORM=xcb

Then start SAMSON in the same terminal. Note, SAMSON is installed in your home directory ~/OneAngstrom/SAMSON-Application/4.0.0/Binaries, you can try starting ./SAMSON-Launcher.sh

If this works, you can try disabling Wayland on your system, for that you will need sudo privileges:

Disable Wayland by uncommenting WaylandEnable=false in the /etc/gdm3/custom.conf Add QT_QPA_PLATFORM=xcb in your ~/.bashrc file.

You might need to restart either the OS or the terminal.

You can check whether your system uses Wayland or X11 by running the following command in the terminal:
echo $XDG_SESSION_TYPE

Hi Chris, thanks again for reaching out! As discussed, this was caused by having ligands with multiple connected components, which Vina cannot dock. We will try to provide clearer error messages to prevent this. Thanks again!

Dear 闽乐 ,

We have fixed some possible issues in Adenita - it should be updated automatically for you. Could you please check whether it works for you?