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.

Thanks for reporting this bug! It's now fixed, and the fix will be available with SAMSON 2020 R2, which will be deployed this monday (may 11, 2020).

Thanks Dear.

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

Adenita needs older versions of SAMSON because it hasn’t been updated yet (you can see this on the element page). You need to reinstall SAMSON and check the box “Install older versions” to install 0.8.5. Also, please check the requirements on the element page.

Currently, it is not possible because the selection filter functionality is not exposed to external elements. We will update it in the upcoming release of SAMSON.

@emmanuel
For now, you can just reapply the Hydrophobicity color scheme (Biology menu > Colorize > Hydrophobicity).

Dear @Oliver ,

We expect it to be fixed in a few weeks.

Dear @charlie,

For now, Adenita is provided only for SAMSON with version not higher than 0.8.5, (see Latest versions section on the module's web-page). So, to use Adenita you will need to install SAMSON 0.8.5.

You can request the newer version from the Adenita developer ( @Elisa ) here: https://forum.samson-connect.net/topic/139/user-support-adenita .

Yes, I could already run it.
Thank you!

Dear @DmitriyMarin
Thank you for your reply!
Yes, that LAMMPS wizard would be wonderful.

Best regards,
Patrik Molnár

Thank you @Rahad !
Do you mean the minimization step in the AutoDock Vina Extended module? What error does it show?

As for ligand libraries, AutoDock Vina Extended module supports libraries with ligands in formats that can be opened in SAMSON, including .pdb, .mol2, .sdf, .xyz, etc, but not .mol and .pdbqt for now. You do not need to import all the ligands in SAMSON, you just need to provide the path to the folder with a ligand library.

Hello,

The issue is that SAMSON was installed as Administor. Can you please try to activate User Access Control (UAC) so that Windows does not install SAMSON as admin? Here's a link about how to do that: https://www.technipages.com/windows-enable-disable-user-account-control-uac

Please set UAC to e.g. "Always notify" (you can set it back to the previous setting afterwards).

0_1586188022427_b58888db-0b85-4f3f-8459-6d51649a09ab-image.png

Then, please restart your computer, and install SAMSON again.

Please let me know how this goes.

Thanks,

Stephane

Thank you.I will contact.

@dmitriymarin Wow this is really great, thank you!!!

Thank you so much for helping me. I tried to link exactly Qt5.12.5 (my own version is 5.14.1) so it works now. Again, thank you so much.

Best regards,

Dong.

Hi,
Sorry for the issue the file was not shipped with the SDK.
See : https://documentation.samson-connect.net/developers/latest/page_installation.html
To launch SAMSON just execute SAMSON-Core after doing the step inside the previous link.

If the file is absent you can create SAMSON-Core.command with the following content

#!/bin/sh

echo "saving context"
SAVED_DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
SAVED_DYLD_FRAMEWORK_PATH=$DYLD_FRAMEWORK_PATH
SAVED_DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH

echo "launching SAMSON-Core"
script_dir=$(cd "$(dirname "$0")";pwd)
cd "$script_dir"

echo "You need to add ~/Qt5.12.5/5.12.5/clang_64/lib folder in your DYLD_FRAMEWORK_PATH or edit this file"

#export DYLD_FRAMEWORK_PATH=~/Qt5.12.5/5.12.5/clang_64/lib or the one corresponding to your setup
export DYLD_LIBRARY_PATH=$script_dir
export DYLD_FALLBACK_LIBRARY_PATH=$script_dir

./SAMSON-Core #available flags --disablenetwork /--import /--logconsole /--logfile "file" /--logdefaultfile

echo "restoring context"
export DYLD_LIBRARY_PATH=$SAVED_DYLD_LIBRARY_PATH
export DYLD_FRAMEWORK_PATH=$SAVED_DYLD_FRAMEWORK_PATH
export DYLD_FALLBACK_LIBRARY_PATH=$SAVED_DYLD_FALLBACK_LIBRARY_PATH

then execute chmod +x SAMSON-Core.command
then execute chmod +x SAMSON-Core

Jocelyn

Thanks Ibrahima! Let us know if we can help in any way.