ADL: multiple proteins

Gavin Seddon gavin.m.seddon at
Wed May 7 01:53:34 PDT 2008

Swarna Deepa Pandian wrote:
> hi Gavin
> I am also trying to dock a single ligand molecule to multiple proteins but
> till now I have not got any sucess. Wat abt you have u tried out anything
> new.?
> thanks
> Ms.Deepa
> On 4/28/08, Gavin Seddon <gavin.m.seddon at> wrote:
>> Hi,
>> Is it possible to dock the same ligand to multiple proteins via the
>> command line?
>> Thanks.
>> Gavin.
>> ________________________________________________
>> --- ADL: AutoDock List  --- ---
> ________________________________________________
> --- ADL: AutoDock List  --- ---
Sorry, no.  I need to protonate 400 proteins first (using whatif).  Then 
I can look at docking.  I am learning to use command line with ad4.

Maybe a script could be written to use the same ligand/grid for the 
proteins.  However, each docking event will generate many output files 
and there are other issues re.

i think it is so difficult if you want to do that,because each time you 
may optimize your proteins to check this autodock result is reasonable.
  if you want to assist on this caculation, as i know ,chen yuzong 
professorin USC of singapore, explored an programme named inverse-dock 
which would meet your research demand. '

I am therefore going to manually do each dock in a separate directory. 
Pls write again.

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