[Dock-fans] Fw: Re: Fw: Re: Fw: Re: Fw: Re: Fwd: Re: Ligand Docking with DOCK6

Francesco Pietra chiendarret at yahoo.com
Wed Apr 23 01:53:54 PDT 2008


Sorry, "-3" in sphere_select command below should be read "-r"



--- On Wed, 4/23/08, Francesco Pietra <chiendarret at yahoo.com> wrote:

> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: Fw: Re: [Dock-fans] Fw: Re: Fw: Re: Fwd: Re:  Ligand Docking with DOCK6
> To: "Scott Brozell" <sbrozell at scripps.edu>
> Cc: "dock-fans" <dock-fans at docking.org>
> Date: Wednesday, April 23, 2008, 1:34 AM
> --- On Tue, 4/22/08, Scott Brozell
> <sbrozell at scripps.edu> wrote:
> 
> > From: Scott Brozell <sbrozell at scripps.edu>
> > Subject: Re: Fw: Re: [Dock-fans] Fw: Re: Fw: Re: Fwd:
> Re:  Ligand Docking with DOCK6
> > To: "Francesco Pietra"
> <chiendarret at yahoo.com>
> > Cc: "dock-fans"
> <dock-fans at docking.org>
> > Date: Tuesday, April 22, 2008, 10:12 AM
> > Hi,
> 
> > There are several issues here.  First a clarification:
> > 
> > receptor_site_file
> > and
> > grid_score_grid_prefix
> > are distinct.
> > In all docking calculations (i.e., orient_ligand ==
> yes)
> > receptor_site_file defines the active site(s).
> > grid_score_grid_prefix represents a special region of
> the
> > receptor;
> > special in that contact or energy scores can be
> computed
> > very quickly
> > for ligands that dock such that the whole ligand is in
> the
> > region.
> > Grids are not used with continuous score;
> > grid_score_grid_prefix is not a Continuous Energy
> Score
> > Parameter;
> > with continuous score cont_score_rec_filename is the
> > receptor.
> 
> OK. Sorry for having posted mixed continuous/grid scoring.
> However, in the computations, the two were treated
> separately, and in accordance with what you write above.
> 
> > 
> > Second I am not sure exactly what you mean by points.
> > It is best to quote verbatim input and output items. 
> Note
> > that
> > relating a .sph file to a showbox margin and Total
> number
> > of grid points
> > is only a crude way to gauge active sites and
> > receptor region sizes.  Grids are not used with
> continuous
> > score;
> > showbox margin and Total number of grid points are
> > irrelevant.
> 
> OK, sorry again as above. Please, see below for continuous
> docking with respect to the number of spheres.
> 
> > 
> > Third if you are uneasy about blindly leaving a long
> > calculation
> > that is producing no output running then ramp up to a
> long
> > calculation, perhaps starting with a scientifically
> useless
> > calc.
> > The main problem was memory consumption; the total
> number
> > of spheres
> > in the receptor_site_file is directly related to
> memory
> > consumption:
> > Take a receptor_site_file and delete half the spheres
> from
> > it;
> > if necessary patch up the number of spheres in the
> header:
> > e.g.,
> > cluster     1   number of spheres in cluster    12
> > run dock measuring the memory usage;
> > if the calculation is too long then stop it; repeat
> this
> > procedure.
> > Eventually, you will get to a quickly running dock
> calc
> > (perhaps
> > terminating without actually docking the ligand).
> > After a couple of steps you will have a formula for
> memory
> > use
> > as a function of the total number of spheres and a
> feeling
> > for
> > computation time.
> 
> I have now carried out continuous docking serial runs (same
> *.in file as before) for the tree, same-family compounds
> already dealt with on present thread, and for which I have
> carried out biochemical experiments as to their interaction
> with the protein. Computations for two situations of 
> 
> sphere_select -i rec.sph -c protein_noH.pdb -a 3421 -3
> radius_in_A
> 
> where 3421 is the strategic atom number where the sphere
> was centered. I use two values of the radius, 23A and 25A.
> In both cases the spheres (568 for 23A and 685 for 25A)
> represent satisfactorily the protein. The 568 spheres
> situation only leaves out protein loops that may safely be
> considered irrelevant to the docking.
> 
> 
> For the 5-rings and 8-rings compounds all (separately
> carried out before) grid docking simulations OK, followed
> by several ns MD with Amber9 after that the complex was
> embedded in a lipidic membrane. For the 13-rings compound
> we are here trying to solve the remaining issues.
> 
> 
> RUNS WITH 568 SPHERES:
> 5-rings-compound 5.7%mem usage
> 8-rings-compound 10.7%mem usage
> 13-rings-compound 27.9%mem usage
> 
> RUNS WITH 685 SPHERES
> 5-rings compound 8.3%mem usage
> 8-rings compound 15%mem usage
> 13-rings compound what () std.::bad_alloc
> 
> %mem usage refers to the available 23GB for the computation
> (NUMA-type MACHINE with 8 logical processors). Although no
> one of these continuous-docking runs was brought to
> completion, I extracted the above data when %mem usage was
> no more increasing.
> 
> It seems to me (correct, please, if I am wrong) % memory
> usage should be considered for "size" of
> sphere_select.sph AND "size" of the ligand.
> 
> > 
> > Fourth maybe your ligand(s) do not DOCK to your
> receptor.
> > Adding rings may produce a ligand that cannot fit into
> a
> > pocket
> > that was a previous active site.  This is research ...
> 
> YES
> 
> 
> > 
> > DOCK is only parallelized over ligands.  With one
> ligand in
> > ligand_atom_file running in parallel is the same as
> running
> > serially. 
> > Start with serial DOCK on a small representative set
> of
> > ligands. 
> > Once you have useful serial 
> > calculation then run a library of ligands in parallel.
> >
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ParallelProcessing
> 
> OK, I have badly overlooked the point. I expected that
> there was parallelization with respect to the receptor,
> too. I was mislead by amber (re)scoring, where all CPUs are
> at work (at least as observed with the 4-CPUs previous
> machine, not yet tried with the 8-CPUs machine). I
> understand that parallelization is the hardest codification
> in these programs.
> 
> Thanks a lot
> francesco
> > 
> > Scott
> > 
> > > --- On Mon, 4/21/08, Francesco Pietra
> > <chiendarret at yahoo.com> wrote:
> > > 
> > > > From: Francesco Pietra
> > <chiendarret at yahoo.com>
> > > > Subject: Re: [Dock-fans] Fw: Re: Fw: Re:
> Fwd: Re:
> >  Ligand Docking with DOCK6
> > > > To: "Scott Brozell"
> > <sbrozell at scripps.edu>
> > > > Cc: "dock-fans"
> > <dock-fans at docking.org>
> > > > Date: Monday, April 21, 2008, 2:10 PM
> > > > --- On Mon, 4/21/08, Scott Brozell
> > > > <sbrozell at scripps.edu> wrote:
> > > > 
> > > > > From: Scott Brozell
> > <sbrozell at scripps.edu>
> > > > > Subject: Re: [Dock-fans] Fw: Re: Fw:
> Re:
> > Fwd: Re: 
> > > > Ligand Docking with DOCK6
> > > > > To: "Francesco Pietra"
> > > > <chiendarret at yahoo.com>
> > > > > Cc: "dock-fans"
> > > > <dock-fans at docking.org>
> > > > > Date: Monday, April 21, 2008, 1:30 PM
> > > > > Hi,
> > > > > 
> > > > > On Mon, 21 Apr 2008, Francesco Pietra
> wrote:
> > > > > 
> > > > > > Good news, I hope. Please see
> below. A
> > quick
> > > > response
> > > > > would be much appreciated in order to
> decide
> > whether
> > > > to
> > > > > continue or stop the calculation. 
> Thanks,
> > francesco
> > > > pietra
> > > > > > 
> > > > > > --- On Thu, 4/17/08, Scott Brozell
> > > > > <sbrozell at scripps.edu> wrote:
> > > > > > 
> > > > > > > First priority is to
> investigate
> > selected_spheres.sph.
> 
> 
>      
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