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 Post subject: Running autogrid...
PostPosted: Fri Jul 17, 2009 8:40 pm 
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Joined: Wed Jul 15, 2009 7:21 pm
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Is there a way to input the grid coords. and no. points of the search volume by simply typing them in or reading them from a file instead of using the GUI tool? I'm having alot of trouble inputing the correct center coords. and no. points using the GUI tool. Also, is there a way to run autodock with multiiple ligands against a given macromolecule instead of doing each one separately? When I clicked on the "load SD file" button the molcules in the file were not selected.
Thanks.
-Wolf.


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 Post subject: Re: Running autogrid...
PostPosted: Fri Jul 17, 2009 9:58 pm 
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wolf wrote:
Is there a way to input the grid coords. and no. points of the search volume by simply typing them in or reading them from a file instead of using the GUI tool?

Please read the section in AutoDock 4.2 User Guide on AutoGrid Grid Parameter File: GPF to learn where and what you need to type to specify the grid coords. and no. points of the search volume. See also:
http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-grid-parameter-files-for-autogrid4
wolf wrote:
Also, is there a way to run autodock with multiiple ligands against a given macromolecule instead of doing each one separately?

You can select multiple ligands from Ligands folder when you run AutoDock Wizard; hold Shift and/or Control key and use left mouse button similar to the way you select a range of text in word processors - http://en.wikipedia.org/wiki/Shift_key
wolf wrote:
When I clicked on the "load SD file" button the molcules in the file were not selected.

I don't understand this part. Could you please describe this in more details? Please attach images if needed. Thanks!

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 Post subject: Re: Running autogrid...
PostPosted: Thu Jul 23, 2009 12:04 pm 
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Joined: Tue Jul 21, 2009 9:49 am
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Hi,
I have somme prblm with running autogrid.
I can't attach shotscreen for explining my conditiond of work (using Upload attachement icon).

Binary autogrid4 file is located in : /usr/local/bin
gpf file is locate in: /home/mezhoud/Bureau/../hsg1-h.gpf



Thanks


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 Post subject: Re: Running autogrid...
PostPosted: Thu Jul 23, 2009 4:36 pm 
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Hi,
Here the adthost.py file:
Code:
hostMacros = {
    'localhost': { 'host' : 'localhost',
         'autogrid' : '/usr/local/bin/autogrid4',
                   'autodock' : 'usr/local/bin/autodock4',
                   'queuetype' : 'int',
                   'userSpecific' : 0 },

    }


[img]

[/img]


Attachments:
File comment: autogrid config
autogrid.png
autogrid.png [ 211.36 KiB | Viewed 4641 times ]
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 Post subject: Re: Running autogrid...
PostPosted: Wed Aug 19, 2009 2:18 pm 
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Hi,
I am having a problem running the Autogrid too, it gives me an [Error 2], which says the path specified for the file name in cmd is not recognized, what could be the possible reason?
Any help greatly appreciated..
Regards,
Rini


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 Post subject: Re: Running autogrid...
PostPosted: Sat Aug 22, 2009 9:58 am 
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Joined: Wed Jul 15, 2009 8:33 am
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check out FAQ
http://autodock.scripps.edu/faqs-help/f ... pen-a-file

MS


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