ADL: autodock 3.05 on linux cluster?

Cyril Bauvais cyril.bauvais at u-psud.fr
Wed Nov 21 08:45:12 PST 2007


Personnally, I have no much interest using parallel implementation of 
Autodock, in research. But fast (and accurate) docking calculation can 
be convenient for teaching. Especially when you see students only one 
afternoon per month.

Cyril Bauvais



Jack Shultz a écrit :
> This might be helpful for my integration through BOINC, if I could breakdown
> the runs on a complex docking problem into discrete workunits, I could
> distribute it over the internet to my volunteers.
>
> Jack
>
> On Nov 21, 2007 9:36 AM, Demet Akten <dakten at halic.edu.tr> wrote:
>
>   
>> I have seen the benefit of parallel processing for docking large ligands
>> such as cyclosporin with around 15 degrees of freedom. Note that my
>> version
>> of parallel processing is to divide a total of 100 runs into 10
>> different jobs.
>> Unfortunately, I do not have any script which can do it automatically.
>>
>>
>> Assist. Prof. Demet Akten-Akdogan
>> Halic University
>> Department of Molecular Biology and Genetics
>> Findikzade, Istanbul, Turkey
>> email: demet.akten at gmail.com
>>
>>
>>
>>
>> On 21.Kas.2007, at 13:40, Yang Ye wrote:
>>
>>     
>>> On 11/21/2007 7:05 PM, Daniel Jana wrote:
>>>       
>>>> On 21/11/2007, Kalidas Y <kalidas.y at gmail.com> wrote:
>>>>
>>>>         
>>>>> Please refer to the parallel autodock:
>>>>>
>>>>>           
>>>> Just out of personal interest... do you use this? Do you see any
>>>> benefit? I do not use Autodock myself but I am in close contact with
>>>> users that do use and their autodock jobs.
>>>>
>>>> In most of their calculations an Autodock calculation takes a few
>>>> hours to finish. On the other hand, for ab initio calculations I am
>>>> used to wait days to weeks (one of our users had to wait three
>>>> months)
>>>> for a result! In a situation like this, it seems reasonable to use
>>>> parallelization. If you need this result to proceed your calculations
>>>> you cannot wait a six months (or one year) for the job to finish.
>>>> But,
>>>> for Autodock calculations I can't see much gain on doing such a
>>>> parallelization.
>>>> There is one case in which it may be useful, if what you want to
>>>> screen a library of compounds. But, for that Autodock also has way of
>>>> proceeding by doing a more shallow test, which separates the good
>>>> from
>>>> the bad instead of (more) accurately saying which is/are the best.
>>>>
>>>> So, the place where I want to get to is. Do (any of) you see the
>>>> *real* need for a parallel Autodock? Could you elaborate a bit, just
>>>> for me to understand...
>>>>
>>>>         
>>> No. I have done screening over 100 compounds. The issue of mass
>>> running
>>> of AD is actually lacking of (automated) post-processing tools, NOT on
>>> the running or performance of autodock.
>>>       
>>>> Thank you very much in advance,
>>>> Daniel
>>>>
>>>> PS - Keep in mind that software, to run on a cluster, does not
>>>> need to
>>>> run on multiple processors for each job. You can put it working for
>>>> each job with one processor and there is no limit on how many
>>>> instances of Autodock could be running in any one cluster.
>>>> PPS - If anyone wants to answer privately I'm ok with that,
>>>> especially
>>>> if the person is willing to reveal a little bit more, privately, then
>>>> to the mailing list. However I think that this could be an
>>>> interesting
>>>> subject to be discussed publicly, to see the real interest on a
>>>> parallel implementation of Autodock. After all, it comes from Scripps
>>>> in a serial version only...
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>>>>
>>>>
>>>>
>>>>         
>>> ________________________________________________
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>>>       
>>
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>>
>>     
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>   



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