Dear all,
I am risking life and limb here, and possibly wining a first row seat
to 'Morten's Inferno' for modelers!
I want a software that will do some docking of a flexible ligand to a
rigid protein model. Consensus google search suggested me to
use AutoDock 4/Vina. (I am looking for free software).
However, what I want to do is 'non-standard': I know from a
crystallographic structure (brrrr....) the position of a Vanadate,
which has to be (give or take)
the position of my phosphate atom in my substrate (I have a
phosphodiesterase). Thus this point should get fixed in space (no
translation, or ideally
restrained translation of some sort), while rotation around it should
be allowed, plus that point should be the 'root' of the torsion tree
of the ligand
to allow it to change conformation around it. AutoDock (but not Vina)
seems to be able to do it in simulated annealing mode, by setting the
translation to 0.
However, my script does not work, there seems to be a bug is s-a mode
(asking for keyword that in for the g-a mode!),
and while I am waiting for some help from their BB (less lively that
ccp4bb as it seems),
would anyone have any other suggestion for a free docking software
that can do what I want to do?
Tassos
