lorenzo.stella wrote:
In my experience, contrary to what was suggested by Oleg's message, an empty ligand file is not acceptable, since I get an error message saying that the ligand has 0 atoms, and the program stops. Am I doing something wrong?
No, you are right. 0 atoms won't work.
You could use a single HD atom instead of a water, exploiting the fact that Vina uses a united-atom scoring function:
Code:
ROOT
ATOM 1 H ZMR d1001 -27.254 15.059 -21.209 0.00 0.00 0.206 HD
ENDROOT
TORSDOF 0
The output you'd get (with side chains) might look like this:
Code:
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 0.0 0.000 0.000
2 0.1 2.755 3.285
3 0.5 1.326 1.821
4 1.0 1.794 2.315
5 1.0 1.826 2.398
6 1.2 1.313 1.871
7 1.6 1.773 2.681
8 1.8 2.028 3.166
9 2.5 1.710 2.184
As expected, the "intermolecular energy" is 0. The other (2+) modes have positive energies, which are due to the less favorable side-chain positions.
I don't know if you could still feed Vina's output into AutoDock 4, and score it there (If you can, you are really exploiting a bug/misfeature in AutoDock 4 - the free energy of binding water, or another small molecule, is supposed to be near 0), but you could try.
You could also try separating the "side chain", and then scoring it as a ligand with
Code:
vina --score_only ...
This is probably better, since the scoring function will be the same as the one used for minimization.
Oleg
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