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    • R

      Normal Mode Analysis -- How to Select Both Receptor and Ligands?
      SAMSON Extensions • normal mode receptor+ligand • • Rudy

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      Stephane

      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.

    • S

      Autodock Vina PDBQT generation
      SAMSON Extensions • • Serena

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      DmitriyMarin

      Dear @Serena ,
      No, we do not use Open Babel or anything else for that. It is done by the AutoDock Vina Extended module.

    • E

      Animation - docking in Gaussian representation
      SAMSON Extensions • • Eva

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      DmitriyMarin

      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.

    • E

      Symmetry Mate editor not seen after installation
      SAMSON Extensions • • Eva

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      Admin

      Awesome, thanks for letting us know!

    • T

      Adenita support for SAMSON 1.0
      SAMSON Extensions • • Tanish

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      DmitriyMarin

      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.

    • G

      Fatal error trying to use Gromacs Wizard : gro file does not have the number of atoms on the second line
      SAMSON Extensions • • Guy

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      Stephane

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

    • S

      GROMACS files not seen
      SAMSON Extensions • • Sherif 0

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      S

      there is RMSF and hydrogen bond

    • E

      [User Support] Adenita
      SAMSON Extensions • • Elisa

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      O

      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

    • O

      SAMSON crashes when I try to select a section of my DNA origami
      SAMSON Extensions • • Olivia

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      DmitriyMarin

      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.

    • O

      Adenita not showing up
      SAMSON Extensions • • Olivia

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      DmitriyMarin

      Great! Thank you for your reply!

    • P

      Autodock Constraints
      SAMSON Extensions • • Philip 0

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      Stephane

      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

    • S

      Autodock Vina Extended problem
      SAMSON Extensions • • Sherif 0

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      S

      Thanks this is very good to know

    • H

      Ligand Receptor Interaction
      SAMSON Extensions • • HUMERA

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      DmitriyMarin

      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

    • V

      Energy profile from P-NEB
      SAMSON Extensions • • Vladimir 1

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      V

      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.

    • J

      Gromacs Wizard Membrane Protein
      SAMSON Extensions • • Jessica

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      Admin

      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.

    • B

      Molecular Dynamics of Protein-CNT(Carbon NanoTubes) Interaction
      SAMSON Extensions • • Ben

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      Stephane

      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.

    • M

      Can't load CIF files
      SAMSON Extensions • • Mario 0

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      M

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

    • E

      Setting pivot point in Arap path
      SAMSON Extensions • • Eva

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      E

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

    • B

      Docking results export
      SAMSON Extensions • • Bartosz

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      H

      Dear @dmitriymarin thank you very much. It works.

    • A

      AutoDock Vina installation
      SAMSON Extensions • • Arturo

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      Admin

      Hello Arturo,

      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.
      Can you please ask your teacher to contact us at contact@samson-connect.net so we can find the best solution to provide access to all students?

      Thanks,
      Stephane