In the first Python script you showed, the LLM you used (did you use Gemini or SAMSON's AI Assistant?) hallucinated and used some non-existent libraries, classes, and functions in SAMSON, which resulted in errors.
We've just updated the Adenita extension: it now sets the nucleotide names as expected by PDB - DA, DC, DG, DT. Now, it should be suitable for export in the PDB format.
Hi @Nicolo-0 ,
No, currently, there is no option to specify that H-bonds in an H-bond group (which is part of a structural model) should be displayed between hydrogens and acceptors - they are drawn between donors and acceptors, since hydrogens might be implicit. However, we can add such an option in the next major release of SAMSON.
But if you want it just for the sake of visualization, then you can try setting hydrogens as donors programatically (via Python). Note that this should be done without calling update() since this will recompute the bonds.
Did you perform other steps (preparation, minimization, equilibration) in GROMACS Wizard before running the production MD (see GROMACS Wizard tutorials)? If not, you might want to try to run them starting from the preparation step.
Could you share the input (all the input files for the step) and resulting files (the corresponding folder into which GROMACS Wizard saved the resulting files, named with a time stamp, e.g. "2024-10-23_09h55m26s-simulate-error") with us so we can try to reproduce the issue and see is the problem?
You don't need to upgrade your whole system; you can try to update it via the above-given commands which will update the packages installed on your system. And if glibc 2.33 is not available with the update you can try to install it from OpenSUSE Tumbleweed.
Possibly, it is not supported with Cycles kernels (from Blender's Cycles) that we ship. We will try to see what we can do here. Or, maybe, the Cycles kernels we ship are not compatible with the CUDA version installed on your OS.
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.
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.
