ADL: If you don't tell lies, at least you don't have to remember what you have said.

manvendra pratap singh manav_phd2007 at
Wed Jan 23 05:14:48 PST 2008

hello depti 
i think u r not covering ur molecules with the grid . so first u should cover the part of ur macromolecule with the grid and run autogrid .
by doing so what happen actually ...this grid will automatecally calculate the part of ur molecule where ligand could bind.
and when u will run autodock . it will automatically dock the ligand to ur macromolecules. this help in finding the active site by doing the blind docking.
u can find ur ligand pdbqt file ..
first u have to set charge to ur molecule and ligand 
u should know what charges u have to fix to ur ligand and what to ur macromolecule.
when u will load ligand ..choose for the pdbqt file searching in the type of file option.
or after setting charge , save ur ligand as pdbqt file ..
 i think this will help u ..
if u have other quarries ask...

----- Original Message ----
From: Deepthi Rajagopalan <deepthi.86 at>
To: autodock-request at; autodock at
Sent: Saturday, 19 January, 2008 1:43:08 PM
Subject: ADL: help

I am using autodock4. I am having problems when i run autogrid. it says
there is some problem with rigid file. could this be due to active site. I
mean.. i dont exactly know the active site of my protein, so I chose some
residue. could it be due to this??
the error message that I get is

/compute/deepthi/AUTODOCK/i86Linux2/autogrid4: ERROR:  can't find or open
receptor PDBQT file "protein_rigid.pdbqt".

/compute/deepthi/AUTODOCK/i86Linux2/autogrid4: ERROR:  Unsuccessful

why is this happening?
please help!!

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