Dmitriy Marin is a research engineer and co-founder at OneAngstrom (1-a.io). He is one of the main developers of SAMSON and many SAMSON Elements.
Dear @Oisin ,
Covalent bonds are created based on the interatomic distances. Maybe the atoms are placed too far from each other? Could you please check the distance between atoms in your system - you can do it using the Measure editor by clicking on two atoms consecutively. Could you please attach a .cif file in which you experience the problem such that we could check it.
By the way, are you referring to .cif for biomolecules (mmcif/PDBx format) or .cif for crystals?
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.
Dear @Olivia ,
Please note that the Adenita extension is not yet available in the latest version of SAMSON. To use Adenita, you will need thus to install an older version of SAMSON (for example 0.8.5 or 0.7.0).
If you don't see any apps in your SAMSON please check if you have an Internet connection.
In what version of SAMSON, you don't see apps and Adenita?
Ok, we will add to GROMACS Wizard the possibility to save GROMACS results in a specified folder in the upcoming days.
You can save the plots directly from GROMACS Wizard.
Dear @Sherif-0 ,
These files are internal files used to perform GROMACS computations in GROMACS Wizard - they are deleted once the job is finished or before the next job is started. The results of the computations are loaded directly in SAMSON.
Do you want to preserve these files?
Dear @Sherif-0 ,
Vina doesn't require and doesn't use assigned partial charges for atoms, quoting the Vina manual: "assigning atom charges is not needed", "AutoDock Vina ignores the user-supplied partial charges" (see http://vina.scripps.edu/manual.html). So there is no need in adding Kollman or Gasteiger charges.
We will add the seed number in the next version. What do you mean by specifying the used algorithm?
Thank you, @Sherif-0 , for your feedback!