ADL: Automating the Autodock

Jack Shultz jshultz at hydrogenathome.org
Fri Apr 3 11:00:20 PDT 2009


Hello,

I am considering an experimental design that would perform virtual
screening using flexible receptors. I've already setup a good system
using the mgltools scripts. Now I am considering the flexible
receptors. When you prepare a flexible receptor you need to specify
which residues should be flexible. I am wondering if there are any
approaches to picking these receptors that would lend themselves to
automation.

Jack

On Fri, Jan 30, 2009 at 5:39 AM, Riad Schulz <rschulz at uni-greifswald.de> wrote:
> Hi Manishi,
>
> use the MGLToolsPckgs from http://mgltools.scripps.edu/
> There are some utilities like prepare_receptor.py, prepare_ligand.py ...
> (usage should be self-explaining).
>
> hope this helps
> Riad Schulz
>
>
> ----- Original Message ----- From: "Manishi Pandey"
> <manishi.pandey03 at gmail.com>
> To: <autodock at scripps.edu>
> Sent: Friday, January 30, 2009 8:59 AM
> Subject: ADL: Automating the Autodock
>
>
>> Dear Sir/Madam,
>>
>> I am a graduate student at Indian Institute of Information Technology,
>> Allahabad, India. I am working upon Autodock for an academic report. For
>> the
>> purpose, I have to do Flexible docking between ligand and protein, and the
>> number of these molecules is quite high. I referred to Virtual Screening
>> tutorial. The tutorial suggest to generate files for the Autogrid and
>> AutoDock using ADT for individual protein which is not a feasible task as
>> the number of receptors for my work are quite high. Is there any other
>> method through which we could automate the generation of files for
>> Autodock
>> and Autogrid also. Kindly give me appropriate suggestions
>>
>> Looking forward for the reply.
>>
>> Manishi Pandey
>> ________________________________________________
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>
> ________________________________________________
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>



-- 
Jack

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