The Molecular Graphics Laboratory Forum

Dear all,

i am very new to AutoDock Vina and with the help of the tutorial I managed to dock several ligands with a protein.
I used the script which is stated in the tutorial. I docked multiple ligands in one time, but the results I obtained, I am not sure how to interpret these.

The results I obtained are the following:

Ligand 1
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -12.0 1.842 6.909
3 -11.7 3.439 9.274
4 -11.7 2.866 6.330

Ligand 2
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -11.9 1.825 6.910
3 -11.6 3.414 9.233
4 -11.6 2.797 6.237

Ligand 3
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -11.1 0.000 0.000
2 -10.7 1.868 3.800
3 -10.7 2.212 5.155
4 -10.4 2.710 4.934
5 -10.3 2.263 5.619

Ligand 4
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -11.1 0.000 0.000
2 -10.7 1.871 3.798
3 -10.7 2.217 5.161
4 -10.5 1.612 4.666
5 -10.4 2.723 4.953

Ligand 5
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -11.9 1.846 6.924
3 -11.7 2.828 6.301
4 -11.6 3.457 9.297

Ligand 6
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -11.9 1.821 6.930
3 -11.7 3.400 9.239
4 -11.7 2.797 6.245

Ligand 7
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -11.9 1.842 6.914
3 -11.6 2.831 6.304
4 -11.7 3.475 9.307

Ligand 8
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -12.0 1.847 6.902
3 -11.7 3.421 9.260
4 -11.7 2.826 6.280

Ligand 9
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -12.0 0.000 0.000
2 -12.0 1.846 6.913
3 -11.7 3.480 9.316
4 -11.7 2.839 6.316

The reference ligand in my case is ligand number 9, how do I select the best ligand similar to ligand number 9? And how do I interpret these results?
Hope someone is able to help me!

Thanks in advance.

Regards
Marja