ADL: error

Filippo Marchioni Filippo.Marchioni at
Fri Aug 3 05:59:47 PDT 2007

Dear Autodock users,

I am trying to switch from Autodock 3 to Autodock 4 on Linux platform
and I am currently following the tutorial.

I have few questions:

Rigid protein-flexible ligand no problem; the docking get successfully
done but I notice that in ADT when I am choosing the ligand during the
grid setting  I don't see the AutoGpf Ligand widget opening up and let
me choose the type of maps to be calculate but instead it only pops up a
widget with this message: "./ind.pdbqt"
Is this normal with ADT 1.4.5? (The version I use is ADT 1.4.5
Unix/Linux x86)

When I tried to set a flexible protein -flexible ligand docking I get
exactly the same problem that I mention before during the grid set but
unfortunately the docking doesn't get completed and when I run Autodock
I get this error message form the log file:

ERROR:  ATOM and HETATM records must be numbered sequentially from 1. 
See line 94 in PDBQT file "ind.pdbqt"

I checked in the ind.pdbqt file and they are actually numbered
sequentially  starting form 1 and the file is only 82 lines long.
Did anyone face the same issue?
Do you have any suggestion?

Thanks in advance


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