Dear Samson,
I am running Auto Dock Vina extended with a library of 7 compounds. I started the run at 9 PM on 11 Nov 2019 and as I send the screenshot of 12 Nov 2019, it just completed 23%. Is it the normal time vina takes in Samson or there is any other issue. My receptor is 379 aa long and it is monomer.

Thank You

It is saying it as a problem. Backing up of file is working anymore. Rest of the log is normal but it got stuck at this point and then nothing works.

My Gromacs session is not working properly. It is always giving the same error.
Sorry couldn't backup C:/Users/Structure/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/MODEL_prepared_model_Ion_chain_C_pr.itp to ./#C:/Users/Structure/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/MODEL_prepared_model_Ion_chain_C_pr.itp.1#
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./amber99sb-ildn.ff/aminoacids.arn
Opening force field file ./amber99sb-ildn.ff/dna.arn
Opening force field file ./amber99sb-ildn.ff/rna.arn

@admin one pdb file having protein and ligand docked.

I would like to save protein with the best conformation of the ligand as a complex but I am not getting it as a normal complex in a single file. kindly help.

Hello,
Kindly provide a tutorial for protein-ligand complex MD simulation in SAMSON.
Also provide guidelines to save and analyze the MD trajectories for data analysis and interpretation (such as RMSD, RMSF, PCA, etc.).
Also, kindly tell me is it possible to simulate the protein-membrane complex in SAMSON? If yes, how?

Hello,
I am running my simulation and selecting the trajectory option to save the result. Is there any way to save the last frame of the trajectory as a gro or pdb file out of the whole trajectory?
This will solve both issues to solve the result as trajectory as well as the last final frame to be used for further analysis.
Kindly also tell where all the results got saved during the whole SAMSON operation (because SAMSON does not ask for choice of directory for saving results)?

Thank You

Thanks a lot. Now it is working in the advanced element of AutoDock (normal one I did not check)
Thank you

Hello,
How can I save the PDB structure of protein-ligand complex (with single desired mode of ligand) in Autodock vina element?
And if I want multiple ligands within a single PDB, how to achieve that?

Dear Stephane,
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.