ADL: Problems with Docking Organometalic Complexes

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ADL: Problems with Docking Organometalic Complexes

جاسم غالب مهدي
Dear all

I would be grateful if anyone could kindly help in resolving some problems
that is associated with using AutoDock ver. 1.5.6 to dock organozinc
complex with a receptor. The first problem occurs in the last step of the
attached AUTODOCK 1.5.6 Tutorial. The message from Command Prompt was
(autogrid4
is not recognized as an internal or external command, operable programme or
batch file). Does autogrid4 need to be installed separately or it is part
of the of the AutoDock main programme.

The second problem is that the organozinc complex breaks down, where zinc
ion split from the molecule. Is there any way to maintain the integrity of
organometablic complex?

As I am knew I also would be grateful if anyone could kindly check the
following attached file:

1. Compressed file which includes receptor.pdbqt, ligand.pdbq,
receptor.gpf, and ligand.dpf.

2. The guideline that was followed in the preparation of the 4 main files
in the Compressed file. The problem occurred in the last step. In which
AutoDock4.exe does not exist.

3. Report by AutoDock software.

With kind regards

Jassem

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

4HBZ.rar (969K) Download Attachment
AUTODOCK 1.5.6_Tutorial.doc (746K) Download Attachment
Report.doc (56K) Download Attachment
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Re: ADL: Problems with Docking Organometalic Complexes

Ruth Huey
You can download autogrid4 and autodock4 here:
http://autodock.scripps.edu/downloads
 
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of جاسم غالب مهدي [[hidden email]]
Sent: Tuesday, May 20, 2014 12:40 AM
To: [hidden email]
Subject: ADL: Problems with Docking Organometalic Complexes

Dear all

I would be grateful if anyone could kindly help in resolving some problems
that is associated with using AutoDock ver. 1.5.6 to dock organozinc
complex with a receptor. The first problem occurs in the last step of the
attached AUTODOCK 1.5.6 Tutorial. The message from Command Prompt was
(autogrid4
is not recognized as an internal or external command, operable programme or
batch file). Does autogrid4 need to be installed separately or it is part
of the of the AutoDock main programme.

The second problem is that the organozinc complex breaks down, where zinc
ion split from the molecule. Is there any way to maintain the integrity of
organometablic complex?

As I am knew I also would be grateful if anyone could kindly check the
following attached file:

1. Compressed file which includes receptor.pdbqt, ligand.pdbq,
receptor.gpf, and ligand.dpf.

2. The guideline that was followed in the preparation of the 4 main files
in the Compressed file. The problem occurred in the last step. In which
AutoDock4.exe does not exist.

3. Report by AutoDock software.

With kind regards

Jassem

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---