[Dock-fans] Fixing protonation state

[burgosgu at ualberta.ca]

Hi everybody,

I need to have a compound correctly protonated to dock it. I tried to  
use the resource of
"upload sets" of ZINC, but it seems that it does not have the required  
charactersitics of
bioavailability and non-toxicity, because it gives me no output as it  
did with other
compounds.

The smile for this compound is:
C1=C(C=CC2=C1C(=C[N]2)CC(=O)NCCCNCCCCNCCCNC(=O)CC3=C[N]C4=C3C=C(C=C4)Br)Br

Any suggestions??

THANKS,

Asdrubal