What about RMSD ?

Question

[chemistry1233]

What about RMSD, how important is and where based it, how calculate rmsd. I use autodock vina, I know that rmsd compare my ligands docking with native from rcsb.org.

but why always first conformation has RMSD 0.00000 and others have 0<RMSD. which must to get as best.

Answer 1

[venu]

Question is somewhat obscure (at least to me).

What about RMSD? You should check this first and I really don't understand what do you mean by where based it. RMSD is a medium to know how much deviation is observed from native conformation after docking has been done . Definitely conformational changes will show up after docking. What do you mean by first conformation and other conformations? Do you mean after docking?

Answer 2

[chemistry1233]

I use autodock vina for docking and I get 9 results (conformations) ranked by energy. and always RMSD for first conformation is 0.000 and for others is RMSD>0.

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1         -7.4      0.000      0.000
   2         -7.4      0.779      1.133
   3         -7.0      1.617      1.993
   4         -6.9     26.631     28.327
   5         -6.6      1.583      1.977
   6         -6.5      3.199      3.974
   7         -6.4      7.415      9.928
   8         -6.3     26.568     27.714
   9         -6.1     27.082     28.571

in this example which I should to get as best binding energy from RMSD value.

comparison happen from ligand-protein complex from rcsb.org and my ligands that I use for docking. but what if my ligand is more active than native ligand

[venu]

Calculate RMSD for every conformation and the native one. The one with the lowest RMSD value from the native conformation is the best one, note the binding energy. Compare binding energy of native conformation and your docked conformation. Based on this single (probably simple) result, you can't say your ligand is more active than native ligand. Autodockvina is a good one but but the perfect one. Compare your results with the results from other docking programs.

Answer 3

[chemistry1233]

Thanks. But why always with vina first conformation has RMSD 0.0000. as in my example. and my question is should I get as best conformation, it that has lowest binding energy and lowest RMSD value (generally RMSD<2 A)

[venu]

You can select the best conformation among the results of autodock vina but not the best conformation for a particular protein. While searching for poses the program keeps the given conformation as it is and starts selection of poses from there. That's why you always get RMSD value 0.