DOCK chem.defn file
Dear CCL users,
the atom labelling parameters used by DOCK (chemical matching option) are
contained in the file chem.defn.There, a set of atom definition rules (based on
.mol2 atom types) is used to define acceptor, donor, polar hydrophobic atoms.
For instance a carboxylate carbon is defined as
C.2 (2 O.co2)
where ( ) specify atoms that must be bounded to the parent atom. Similarly [ ]
specify atoms that must not be bound to the parent atom. (*) specify any atom
type (page 96 of the manual).
Looking at the chem.defn file (page 98 of the manual) it contains, for instance,
entries such as:
F [*] for polar
C.3 [*] for hydrophobic
O. [H] [N.] (*) for acceptor
The way I read these entries is:
F [*] = a fluorine atom with nothing attached to it
C.3 [*] = an sp3 carbon with nothing attached to it
O. [H] [N.] (*) = any kind of oxygen with any atom attached to it but H or N
Clearly it is not possible that DOCK is defining the labels as isolated fluorine
or carbon atoms as it is not possible that the definition of acceptor does not
include -OH. Any better way to interpret these definitions?
Thank you very much.