[Dock-fans] GBSA rescoring error

Rima Chaudhuri rima.chaudhuri at gmail.com
Fri Sep 13 00:57:57 PDT 2002


Thanks Sudipto!
I upgraded to 6.1 and am running the Grid based score calculations now. I
plan to rescore the results with gbsa_hawkins. My question is pertaining to
your comment that we do not need grids for the gbsa calculation..I was under
the impression that we need to compute the solvent grids for the gbsa
part..if that is not the case then when do we need the solvent grids at
all??

thanks,
Rima
On 4/30/07, Sudipto Mukherjee <sudmukh at yahoo.com> wrote:
>
>  Rima,
>
> First, I strongly recommend you upgrade to DOCK 6.1. The GBSA hawkins
> scoring should only be done on the actual receptor coordinates, and not with
> a grid. For grid-based solvent scoring, please refer to the Zou gbsa scoring
> section in the manual. Further, since all-atom hawkins gbsa scoring is a
> slow process, docking or minimizing (which could involve scoring thousands
> of structures) is NOT recommended for this scoring function. It is only
> meant to be used to rescore final docked and minimized poses to obtain a
> better binding energy estimate than the default DOCK score. I recommend you
> dock in your ligands with standard ES+VDW grid based score, and subsequently
> rescore your best poses with the Hawkins gbsa score.
>
> The bump filter in dock6.0 versions was rejecting conformations too
> harshly, and is the likely reason why dock said "Could not complete growth".
> In dock6.1, the bump filter code was significantly changed (see
> http://dock.compbio.ucsf.edu/DOCK_6/6.1/new_in_6.1.txt).
>
> Regards
> Sudipto Mukherjee
> Graduate Student, Robert C. Rizzo Lab
> Dept. of Applied Math & Statistics, Stony Brook University
> Lab: 631-632-8519, Mobile: 631-220-5744
>
>
> ----- Original Message ----
> From: Scott Brozell <sbrozell at scripps.edu>
> To: Rima Chaudhuri <rima.chaudhuri at gmail.com>
> Cc: dock-fans at docking.org
> Sent: Thursday, April 19, 2007 12:48:31 AM
> Subject: Re: [Dock-fans] GBSA rescoring error
>
> Hi,
>
> On Wed, 18 Apr 2007, Rima Chaudhuri wrote:
>
> > Yes, I did try GBSA for a single molecule using the serial version. The
> same
> > problem occurs.It gives the same error, as in "Could not complete
> growth..."
> > The size of the files are such:
> >  938092      solvent_gbsa_grid.bmp
> >  11256736  solvent_gbsa_grid.nrg
> >  5420 Apr   solvent_gbsa_grid.out
> >  1148192    solvent_grid.bmp
> >
>
> These are not big files and if serial dock6 gives the same behavior
> as parallel dock6 then I do not understand the slow (9 hr) startup time.
>
> I notice that the input file below uses bump filtering and the
> dock version is 6.0.  Did your initial grid score calculation use
> bump filtering ?
> Try turning off bump filtering:
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-August/000694.html
> or upgrading to dock 6.1:
> (there have been changes to the bump filter in version 6.1)
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-December/000827.html
>
> Scott
>
> > On 4/18/07, Scott Brozell <sbrozell at scripps.edu> wrote:
> > >
> > > On Mon, 16 Apr 2007, Rima Chaudhuri wrote:
> > >
> > > > I am trying to rescore a set a ligands using GBSA_hawkins. The
> ligands
> > > were
> > > > intially scored using grid score which worked fine.
> > > > In the absence of a tutorial I am not too sure if I am even doing
> the
> > > right
> > > > thing in terms of rescoring DOCK Runs with Solvation Scoring
> Functions.
> > > I
> > > > used the file solvent_grid.in
> > > > (/dock6/bin/tutorials/solvent_scoring_demo/solvent_grid.in) as the
> > > template
> > >
> > > tutorials/solvent_scoring_demo/3_grid/solvent_grid.in
> > > is a reasonable template.
> > >
> > > > for generating the solvent grid from my usual .sph file. I created a
> box
> > > > using showbox with extra margin of 5A, just to make sure the box is
> big
> > > > enough. On running dock6.mpi, the job reads the solvent grid files
> for
> > > over
> > > > 9 hrs and then gives the following output: ERROR: could not comlpete
> > > growth
> > >
> > > The long startup time might indicate that the grid file is too big.
> > > What is the file size ?
> > > Did you try a single ligand run with serial dock6 ?
> > >
> > > Scott
> > >
> > > > Please let me know if I am missing something here.  Thanks for your
> > > help.
> > > >
> > > > DOCK v6.0
> > > >
> > > > Released June 2006
> > > > Copyright UCSF
> > > > --------------------------------------
> > > >
> > > >
> > > > Molecule Library Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > ligand_atom_file
> > > > ./lead_like_conf_ranked.mol2
> > > >
> > >
> ligand_outfile_prefix                                        gbsa_hawkins
> > > > limit_max_ligands                                            no
> > > > read_mol_solvation                                           no
> > > > write_orientations                                           no
> > > > write_conformations                                          no
> > > > skip_molecule                                                no
> > > > calculate_rmsd                                               no
> > > > rank_ligands                                                 yes
> > > > max_ranked_ligands                                           9000
> > > > scored_conformer_output_override                             no
> > > >
> > > > Orient Ligand Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > orient_ligand                                                yes
> > > > automated_matching                                           yes
> > > > receptor_site_file
> > > > ./final_spheres.sph
> > > > max_orientations                                             500
> > > > critical_points                                              no
> > > > chemical_matching                                            no
> > > > use_ligand_spheres                                           no
> > > >
> > > > Flexible Ligand Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > flexible_ligand                                              yes
> > > > min_anchor_size                                              15
> > > > num_anchor_orients_for_growth                                25
> > > > number_confs_for_next_growth                                 25
> > > > use_internal_energy                                          no
> > > > use_clash_overlap                                            no
> > > >
> > > > Bump Filter Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > bump_filter                                                  yes
> > > > bump_grid_prefix
> > > > solvent_gbsa_grid
> > > > max_bumps                                                    2
> > > >
> > > > Master Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > score_molecules                                              yes
> > > >
> > > > Contact Score Paramters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > contact_score_primary                                        no
> > > > contact_score_secondary                                      no
> > > >
> > > > Grid Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > grid_score_primary                                           no
> > > > grid_score_secondary                                         no
> > > >
> > > > Dock3.5 Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > dock3.5_score_primary                                        no
> > > > dock3.5_score_secondary                                      no
> > > >
> > > > Continuous Energy Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > continuous_score_primary                                     no
> > > > continuous_score_secondary                                   no
> > > >
> > > > Zou GB/SA Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > gbsa_zou_score_primary                                       no
> > > > gbsa_zou_score_secondary                                     no
> > > >
> > > > Hawkins GB/SA Score Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > gbsa_hawkins_score_primary                                   yes
> > > > gbsa_hawkins_score_secondary                                 yes
> > > >
> > >
> gbsa_hawkins_score_rec_filename                              ./protein2.mol2
> > > > gbsa_hawkins_score_solvent_dielectric                        78.5
> > > > gbsa_hawkins_use_salt_screen                                 no
> > > > gbsa_hawkins_score_gb_offset                                 0.09
> > > > gbsa_hawkins_score_cont_vdw_and_es                           no
> > > > gbsa_hawkins_score_grid_prefix
> > > > ./solvent_gbsa_grid
> > > >    WARNING:  Grid file should have been prepared with
> > > >    "distance_dielectric = no" and "dielectric_factor = 1"
> > > >
> > > > Simplex Minimization Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > minimize_ligand                                              no
> > > >
> > > > Atom Typing Parameters
> > > >
> > >
> ------------------------------------------------------------------------------------------
> > > > atom_model                                                   all
> > > > vdw_defn_file
> > > > /n4/rima_temp/dock6/parameters/vdw_AMBER_parm99.defn
> > > > flex_defn_file
> > > > /n4/rima_temp/dock6/parameters/flex.defn
> > > > flex_drive_file
> > > > /n4/rima_temp/dock6/parameters/flex_drive.tbl
> > > >
> > > > Initializing Library File Routines...
> > > > Initializing Orienting Routines...
> > > > Initializing Conformer Generator Routines...
> > > > Initializing Bump Filter Routines...
> > > >  Reading the bump grid from solvent_gbsa_grid.bmp
> > > > Initializing Hawkins GB/SA Score Routines...
> > > > Initializing Grid Score Routines...
> > > >  Reading the energy grid from ./solvent_gbsa_grid.nrg
> > > > DOCK is currently running on nike.structure.uic.edu
> > > >
> > > > -----------------------------------
> > > > Molecule: ZINC04543170
> > > >
> > > >  Elapsed time:  6653 seconds
> > > >
> > > >  ERROR:  Could not complete growth.
> > > >          Confirm grid box is large enough to contain
> > > >          ligand and try increasing max_orients.
> > > >
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>
>
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-- 
-Rima
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