ADL: search space parameters in vina

yanyuna hiyanyuna at gmail.com
Tue Nov 26 19:34:45 PST 2013


On 2013年11月26日 22:25, yanyuna wrote:
>
> On 2013年11月26日 21:39, Brian Moldover wrote:
>> If the structure is liganded, center the box on the ligand and expand 
>> the
>> search space to cover the ligand, plus maybe 2 angstroms on all sides 
>> to be
>> safe. If the liganded structure is solved, and you know the interacting
>> residues, you can draw the smallest box possible that captures those
>> interacting residues, and the center can be determined by that box.
>>
>> It's a little trial and error, although Vina is not that sensitive to 
>> where
>> you center the search space. What's important is to capture the 
>> binding site
>> information.
>>
>> -Brian
>>
>> -----Original Message-----
>> From: autodock-bounces at scripps.edu 
>> [mailto:autodock-bounces at scripps.edu] On
>> Behalf Of Jiza Formeca
>> Sent: Monday, November 25, 2013 10:27 PM
>> To: autodock at scripps.edu
>> Subject: ADL: search space parameters in vina
>>
>> Hi
>> Anyone has good advice for determining the search space parameters in 
>> vina?
>> I need help with center_x, center_y, and center_z.
>>
>> Jiza
>> ________________________________________________
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>>
>> ________________________________________________
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> Hi ,
> Thank you for your reply. I want to search the whole protein to find 
> all the possible binding sites. The small molecular is not a liganded 
> ligand , but a small probe I construct myself . So I want to center 
> the box on the protein . But I don't know how to save 2000 conformation ?
Hi,
   Does anyone know whether the result of vina has been clustered like 
autodock4 or not ?


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