CCL: Autodock - Questions

 Sent to CCL by: "Eliac  Brown" [Eliacbrown*]
 Dear All
 I wan wondering if someone here could help me throughout autodock. I sent my
 email to autodock list, but I haven't got any reply.
 Here is my email, please any kind of help would be highly appreciated.
 Dear ALL
 I couldn't understand some terms in Autodock, and I need a help please:
 * setminmax is a function to definethe minimum and maximum bond length
 between a couple of atoms, what is the aim of this function, as I believe
 autodock doesn't minimize the ligand structure?
 * How can I define explicity the setminmax in autodock tools? I need to make
 the bond between H-X constant, how?
 * What is the diffence between "Donor S Spherical Hydrogen" and
 "Donor 1 H-
 bond Hydrogen"?
 * How can I switch between Amber parameters and autodock parameters
 * I am developing a new hydrogen atomtype, if I used XX atom type, the
 hydorgen bond will not be a directional bond, I couldn't replace the HD
 parameters with the new one where I am going to use both of them at the same
 time in the same molecule, what would you recommend?
 * I couldn't find reference for the volume and solvation parameter
 calculation, how you get these values for hydrogen (for example)?
 * partial charges: When I assigned partial charges of my protein using
 kollman method (all hydrogen explicit) and compared it to AMBER partial
 charges (using amber99SB force field), I found they are different, why?
 * Non-polar hydrogens are merged into the borne atom, in these case we call
 it united atom, how it is charge calculated? by adding the charge of the
 hydrogen atoms to the mother atom? if so, why the charge of the polar
 hydrogens are different between the two calculations?
 Please, any kind of help would be appreciated.
 Thanks in advance