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?
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.
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.
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):
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.
thanks for your interest in SAMSON!
The AutoDock Vina element has been deprecated as it was offering limited functionality (only one ligand at a time). It is still possible to use the AutoDock Vina Extended element for free for 30 days (no credit card needed) and it can do more, including pre-minimization of ligands and docking entire libraries.
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