Subject: CCL: AutoDock parametrisation - some big questions

From: Arturas Ziemys <[email-masked]>
Date: Thu, 12 Jul 2001 09:37:14 +0200 (GMT)

Hi, CCL'ers,

AutoDock 3.0.5 parametrisation is unclear still:

1) I docked Fe anionic complex (-2) to some protein. Fe atom type
parameters were included manually as it was suggested in AutoDock
homepage. My docking energies were possitive. 

Could it be ? What is wrong ? 
Have anybody tested compound docking with Fe atom wit AD 3.x ?

2) Grid Paremter File (GPF) contains "sol_par" and "constant" keywors
after each grid map 7 lines of interactions. I didn't came accross the
purpose of these keywrds in manual.

Could anybody explain the purpose of these keywords ?

3) Script utillities automatickly ganerates GPF with H-bond parameters
assigned to O and S atom types with H. 

Why that do not happen with N ????

Looking forward for suggestions and any elucidations.
Best wishes

Arturas Z.