ADL: grid dimentions

Rudy J. Richardson rjrich at umich.edu
Wed Sep 22 10:38:57 PDT 2010


Nok and Hamed:

It is my understanding that autodock and autogrid use a default grid 
spacing of 0.375 A and a maximum of 128 grid points for each dimension. 
Therefore, the maximum length of each dimension of the grid box is 0.375 A 
x 128 = 48 A. If you change the default grid spacing, you can get larger 
grid boxes, but with less accuracy for docking. If you know the region of 
the active site, you can draw the box to cover this region. However, if 
you want to cover an entire protein that does not fit into a 48x48x48 A^3 
box, you can follow the instructions in the manual to construct more than 
one grid box or use third-party software to combine grid boxes.

Best regards,

Rudy

Rudy Richardson
University of Michigan

On Wed, 22 Sep 2010, Nok :p wrote:

>
> Dear Dr. Hamed Ismail
>
>
>
> You can modify the size of grid box by:
>
>
>
> Grid -> grid box-> you will see the wheel of x, y, z that you can modify the size of grid box
>
>
>
> then you will save the new dimention by:
>
>
>
> File -> close saving current
>
>
>
> Alternative way, you can also modify the size of grid in the file.gpf
>
>
>
> Best regards,
>
>
>
> Jiraporn
>
>> Date: Tue, 21 Sep 2010 14:58:30 -0700
>> From: hamed_ali37 at yahoo.com
>> To: autodock at scripps.edu
>> Subject: ADL: grid dimentions
>>
>> Dear colleagues
>> Kindly tell me How to modify my grid dimentions in AutoDock 4.2 version as
>>  I already used 85 angestroms for each direaction in grid box option, However after Autogrid I got results as:
>> Number of grid points in x-direction: 65
>> Number of grid points in y-direction: 65
>> Number of grid points in z-direction: 65
>>
>> Please help me how to change that to get higher dimentions
>> Best reagrds
>> Dr. Hamed Ismail
>>
>>
>> --- On Tue, 9/21/10, autodock-request at scripps.edu <autodock-request at scripps.edu> wrote:
>>
>>
>> From: autodock-request at scripps.edu <autodock-request at scripps.edu>
>> Subject: autodock Digest, Vol 73, Issue 14
>> To: autodock at scripps.edu
>> Date: Tuesday, September 21, 2010, 3:00 PM
>>
>>
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>> Today's Topics:
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>>    1. Re:  Method of covalent docking (Nok :p)
>>    2. Re:  Method of covalent docking (hamze rahimi)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 21 Sep 2010 02:45:48 +0000
>> From: "Nok :p" <justmin28 at hotmail.com>
>> Subject: Re: ADL: Method of covalent docking
>> To: autodock <autodock at scripps.edu>
>> Message-ID: <BAY146-w1089AED398A9C930A7EAEDB77F0 at phx.gbl>
>> Content-Type: text/plain; charset="windows-874"
>>
>>
>> Dear Rudy,
>>
>>
>>
>> Thanks you very much for your good suggestion.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Nok
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 21 Sep 2010 00:32:23 -0700
>> From: hamze rahimi <buksanbio at gmail.com>
>> Subject: Re: ADL: Method of covalent docking
>> To: autodock at scripps.edu
>> Message-ID:
>>     <AANLkTinzjGTi8Wb=p94XT=KiCdD9MLfhO4UO0=+r-s3u at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear expert
>>
>> hi.you can use GROMACS or NAMD package for MD of proteins.then resulted dpb
>> introduce for docking.
>> best wish
>>
>> 2010/9/20 Nok :p <justmin28 at hotmail.com>
>>
>>>
>>> Dear Rudy,
>>>
>>>
>>>
>>> Thanks you very much for your good suggestion.
>>>
>>>
>>>
>>> Best regards,
>>>
>>>
>>>
>>> Nok
>>>
>>>
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>>
>>
>>
>>
>> --
>> Yours sincerely
>> Rahimi Hamzeh
>> PhD student in Medical Biotechnology
>> Pasteur institute of iran
>> e mail:
>> buksanbio at gmail.com
>> hamzebiotech at gmail.com
>> Tel: 09125975321
>>
>>
>> ------------------------------
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>>
>> End of autodock Digest, Vol 73, Issue 14
>> ****************************************
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>>
>>
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