Subject: autodock cryst.str. minimisation

From: Robert Soliva <[email-masked]>
Date: Tue, 23 Oct 2001 06:10:13 +0200

Dear Autodock users,

I have a couple of questions regarding the use of autodock to minimise
with the local search method. I apologise if
they seem too obvious (I have just started using the program).

1- I want to minimise a ligand-receptor structure taken from the pdb. I
understand I am supposed to use the do_local_only
command,  but I do not know how to tell the program to optimise without
moving the ligand randomly out of the active site.
Could anybody send me an example of a dpf input file that can do this?

2-Is is possible once the minimisation has taken place, to have not only
the value for the total interaction, but also the value
for the different terms of the scoring function (i.e. to have the value
and its composition in terms of vdW, electrostatic, H bonding
torsion and desolvation?). Is there a command to ask the program for
those values?

Please reply to [email-masked]

Thank you very much for your help.

Robert.