SAMSON Extensions

Hi @Federico-Maria , Sorry about the issue. Currently, SAMSON supports virtual reality only for the Windows Mixed Reality headsets. The virtual reality feature for Meta headsets is not yet available.

@Federico-Maria , Great! Thanks for checking! Thanks for mentioning, the thing in 'About SAMSON' will be fixed with the next patch release of SAMSON.

We have posted a brief tutorial on preparing protein-ligand systems with GROMACS Wizard. We will add more information to it over time, specific to each parametrization tool/server.

Dear Michael, I fixed the issue in the GROMACS importers (trajectories, .gro) on macOS that was causing the options to be disabled and was also affecting the GROMACS Wizard. Could you please check whether the GROMACS Wizard and loading of GROMACS trajectories now work for you?

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 @Eva , We have improved the performance of surface visual models (Gaussian, Solvent Accessible, and Solvent Excluded surfaces) in certain cases. For example, now animations with them should be much faster. The visual models should be automatically updated for you once you restart SAMSON.

Awesome, thanks for letting us know!

Dear @Tanish , Adenita is a third-party extension developed by external developers. Since it is open-source, we started porting it ourselves to the latest SAMSON. The latest SAMSON compared to the versions of SAMSON which support Adenita has a lot of major changes meaning that the porting process will take quite some time especially together with fixing some issues in Adenita. Currently, we cannot give a time estimate since we work on it occasionally in our free time, but we hope it will be ready in the upcoming months. We are sorry about the inconvenience.

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

there is RMSF and hydrogen bond

I have a structure I would like to alter a bit using Adenita, but whenever I try to select it, it becomes non-responsive and crashes. I've tried using a .json file and a .pdb file and neither is capable of having parts selected. I tried on two different computers, one with a quad-core and one with a 6-core and it still crashed. Is there a way I can perform this on my build? Or is this a software issue that others experienced? OS: Windows 10 Ver: SAMSON 0.8.5

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 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

Thanks this is very good to know

Dear @Mariangela , To find and show hydrogen bonds you can use the Hydrogen Bond Finder Extension. It allows you to find all H-bonds in the selected system or between two systems, for example, between a receptor and a ligand. To find/show H-bonds between a receptor and a ligand, perform the following steps (see the gif at the end): in the Hydrogen Bond Finder Extension click on "...in the current selection and the system"; select the receptor in the Document view and in the Hydrogen Bond Finder click Set; [image: 0_1607705913844_07ee1a78-6dba-4dcc-912b-bf40a6d8a6fa-image.png] set the Settings of the Hydrogen Bond Finder if necessary; now, select only the ligand in the Document view and in the Hydrogen Bond Finder click Add hydrogen bond visual model Now you should have a new visual model in the Document view. If you select it, you can modify its options in the Inspector. See an example below: [image: alt text]

Yes, it would be useful to have the energy profile along the path. Not only the height of the barrier, but also its width, shape, etc.

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.

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.