Hi,
I did a docking between protein and ligand using Autodock Vina. In terminal, I try to run and I got three variables i.e. Energi, rmsd l.b., and rmsd u.b. .
1. What is difference between rmsd l.b., and rmsd u.b.?
2. How can I find the pose score of ligand?
3. What actually is the main mathematical model that is used in Vina to get conformational bind?
thanks in advance.
i would start here, http://vina.scripps.edu/, before starting to use Autodock Vina.
Dear Aswin Abbas ,
Usually when you run from your terminal, at the end of the program you can see your results listed in order {1 ... n} where the top 1 is the pose adopted by the ligand with the highest score identified with the most negative union affinity than the others, if you want to get only the best pose, then make the ligand-receptor complex, you can use vina_split to divide it and then use the command "$ cat ligando.pdb receptor.pdb> complex.pdb" and then open it in pymol or another viewer. Good luck,
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