Greetings Sir! I hope you are doing well. Really impressed from your hard work. I have no words to appreciate your efforts. Respected Sir would you like to upload a tutorial regarding calculations of mechanical properties(elastic properties, bulk Modules etc)via SIESTA. Your help in this regards will be highly appreciated. Regards
My ligand has 16 rotatable bonds but ADT set max TORSDOF to 11, is there any way to dock my ligand in Autodock vina where all 16 rotatable bonds are active?
Please answer me, Number of torsions of my ligand is 0 How can I fix it ?! I downloaded the ligand from pubchem as sdf format and covert it to pdbqt And then tried to convert it to pdb and the same result ...
Greetings Sir!
I hope you are doing well. Really impressed from your hard work. I have no words to appreciate your efforts.
Respected Sir would you like to upload a tutorial regarding calculations of mechanical properties(elastic properties, bulk Modules etc)via SIESTA.
Your help in this regards will be highly appreciated.
Regards
Thank you! Yes I am now doing this series of bioinformatics tutorials. Once I complete I will make a tutorial on mechanical properties using Siesta.
respected sir, please make video on molecular dynamics simulation
Great effort! If we are docking nanoparticles, is there any additional steps to consider?
Thank you
Yes, absolutely. You need to parametrise the nanoparticle that you are using for docking. Just update the AD4_parameters.dat.
My ligand has 16 rotatable bonds but ADT set max TORSDOF to 11, is there any way to dock my ligand in Autodock vina where all 16 rotatable bonds are active?
You can set TORSDOF max upto 32 and minimum 8 I guess.
Please answer me,
Number of torsions of my ligand is 0
How can I fix it ?!
I downloaded the ligand from pubchem as sdf format and covert it to pdbqt
And then tried to convert it to pdb and the same result ...
You can set torsions by selecting the main carbon atom and set your torsions.