ADL: autodock 3.05 on linux cluster?

Jack Shultz jackygrahamez at gmail.com
Wed Nov 21 07:13:56 PST 2007


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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> > mailing_list ---
>
>
>
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