Subject: DOCK chem.defn file

From: "Zuccotto, Fabio" <[email-masked]>
Date: Fri, 7 Jul 2000 13:54:47 +0100

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.

fabio