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

Hi Nick, thanks for the posts, we've sent you messages about how to reach us for chat so we can help you.

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;
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:

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.

Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).

First, you will need to modify SAMSON preferences (Ctrl+K):
-1- For the Add editor, disable the "Adjust hydrogens ..." option.
0_1600418725406_Preferences-Add-no-adjust-H.png

-2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.
0_1600418739623_Preferences-Minimize-no-H-warning.png

Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.

@aaa Thank you for reporting your solution here!

Hi James, thanks for reporting this. We sent you an email to determine the issue.

Okay, Thanks.

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.

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.

@dmitriymarin @admin It actually was this. Thanks for solving the problem!

Thank you, Stephan. I will give it a try.

Dear @dmitriymarin thank you very much. It works.

Thank you @Emmanuel for reporting these issues. We have fixed them - the Elements will be updated automatically once you launch SAMSON.

Dear @Emmanuel ,

Thanks for reporting this issue! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed in a few days.