ADL: regarding docking

Ravi Sharma ravi_pharma_biotech at
Thu Jun 11 07:02:48 PDT 2009

I am new to this concept , please help me.
I need to know something regarding docking :-

1. Before running Autodock, am i supposed to go for energy minimization for receptor ?
if yes please tell me parameters to be selected for the same. 

2. How to prepare flexible residue file for flexible docking? In the manual of autodock they mentioned to select ARG8 residue to be flexible. I am using HIV-RT enzyme/receptor for docking. Now, i don't know which residue to select to make flexible. (moreover at position 8 there is no ARG) ?

3. what is the criteria to set Grid properties i.e., Grid dimension, spacing,center?

Ravi Sharma 
B-Pharmacy (Reg.Pharmacist)

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