[Dock-fans] dock 3.6 error

John Irwin jir322 at gmail.com
Tue Sep 17 08:39:17 PDT 2013


Hi Li

We do not distribute the flexibase files with DUD,  We make them ourselves
when we need them using the usual procedure (mol2db, INHIER) that you would
use if you used DOCK 3.6 to prepare databases.

John



On Thu, Aug 9, 2012 at 11:02 AM, Li Huang <lihuang430 at gmail.com> wrote:

> Ryan,
>
> Thanks for the quick reply.
>
>  Actually, I'm trying to reproduce some data done by the DUD database:
> http://dud.docking.org/r2/
>
>  From DUD website, I can download sdf and mol2 files for each target, but
> then how can I convert these file to db.gz files needed for dock3.5.54?
>
> Many thanks
>
> 2012/8/9 Ryan G. Coleman <rgc at blur.compbio.ucsf.edu>
>
> DOCK 3.5/6 use gzipped db files for docking, not mol2 files. The
>> easiest way to get these files is to download them from ZINC using the
>> Flexibase download option on any molecule page.
>>
>> http://zinc.docking.org/
>>
>> http://zinc11.docking.org/fget.pl?l=0&z=91931138&f=h
>>
>> -Ryan
>>
>> On Thu, Aug 9, 2012 at 10:43 AM, Li Huang <lihuang430 at gmail.com> wrote:
>> > Hi guys,
>> >
>> >   I have a question about dock3.5.54, when I try to run a docking, I
>> > assigned "ligand_atom_file"  to  ligands.mol2, and I was told a gz file
>> is
>> > needed. Then I gziped this mol2 file, and got another error "
>>  unsupported
>> > due to backspace call 3.0".
>> >
>> >   Does anyone know what is this related to?
>> >
>> >   I'm using dock3.5.54 because I want to reproduce some old data using
>> the
>> > dock3.5 score.
>> >
>> > Thanks
>> >
>> > _______________________________________________
>> > Dock-fans mailing list
>> > Dock-fans at docking.org
>> > http://mailman.docking.org/mailman/listinfo/dock-fans
>> >
>>
>
>
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>
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