[Dock-fans] Fwd: Re: Ligand Docking with DOCK6
Scott Brozell
sbrozell at scripps.edu
Mon Mar 31 16:11:54 PDT 2008
Hi,
On Sat, 22 Mar 2008, Francesco Pietra wrote:
> While waiting for a clarification about the manual indication for continuous
> score "Regardless of the exponent used, the same radii and well-depths are
> used", I have tried a rigid docking on the same system (protein and large
> ligand) by neglecting the information on radius 25A for the sphere used for
> building the grid.
see
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-March/001489.html
> mpirun -np 4 dock6.mpi -i rigid_nogrid.in -o rigid_nogrid.out
>
> again led to segmentation fault, though less rapidly than when using grid. In
> the few seconds inter lapsed, I had the opportunity to look at "top -i: the
> memory used was 0.1% on all four processors (each used 100%).
>
> Input rigid_nogrid.in:
>
> ligand_atom_file /home/francesco/dockwork/ligand.mol2
> limit_max_ligands no
> skip_molecule no
> read_mol_solvation no
> calculate_rmsd no
> orient_ligand yes
> automated_matching yes
> receptor_site_file /home/francesco/dockwork/selected_spheres.sph
> max_orientations 1000
> critical_points no
> chemical_matching no
> use_ligand_spheres no
> flexible_ligand no
> bump_filter no
> score_molecules yes
> contact_score_primary no
> contact_score_secondary no
> grid_score_primary no
> grid_score_secondary no
> grid_score_rep_rad_scale no
> grid_score_vdw_scale no
> grid_score_es_scale no
> grid_score_grid_prefix no
> dock3.5_score_secondary no
> continuous_score_primary yes
> continuous_score_secondary no
> cont_score_rec_filename /home/francesco/dockwork/protein.mol2
> cont_score_att_exp 6
> cont_score_rep_ex 12
> cont_score_dielectric 4.0
> cont_score_vdw_scale 1
> cont_score_es_scale 1
> gbsa_zou_score_secondary no
> gbsa_hawkins_score_secondary no
> amber_score_primary no
> amber_score_secondary no
> minimize_ligand yes
> simplex_max_iterations 1000
> simplex_max_cycles 1
> simplex_score_converge 0.1
> simplex_cycle_converge 1.0
> simplex_trans_step 1.0
> simplex_rot_step 0.1
> simplex_tors_step 10.0
> simplex_final_min no
> simplex_random_seed 0
> atom_model all
> vdw_defn_file /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file /usr/local/dock6/parameters/flex.defn
> flex_drive_file /usr/local/dock6/parameters/flex_drive.tbl
> ligand_outfile_prefix rigid_nogrid
> write_orientations no
> num_scored_conformers_written 1
> rank_ligands no
This file is still missing e.g.,
cont_score_rep_rad_scale
so verify the final input file; (note dock may write to the input file).
I'd make the first run a serial interactive one.
> The screen output was the same as on the failed rigid dock using grid:
This could mean that your active site representation is the culprit.
Scott
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
> [deb64:03626] *** Process received signal ***
> [deb64:03626] Signal: Aborted (6)
> [deb64:03626] Signal code: (-6)
> [deb64:03626] [ 0] /lib/libpthread.so.0 [0x2b1d13ba0410]
> [deb64:03626] [ 1] /lib/libc.so.6(gsignal+0x3b) [0x2b1d13cd807b]
> [deb64:03626] [ 2] /lib/libc.so.6(abort+0x10e) [0x2b1d13cd984e]
> [deb64:03626] [ 3]
> /usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114)
> [0x2b1d13843424]
> [deb64:03626] [ 4] /usr/lib/libstdc++.so.6 [0x2b1d138415a6]
> [deb64:03626] [ 5] /usr/lib/libstdc++.so.6 [0x2b1d138415d3]
> [deb64:03626] [ 6] /usr/lib/libstdc++.so.6 [0x2b1d138416ba]
> [deb64:03626] [ 7] dock6.mpi [0x42c654]
> [deb64:03626] [ 8] /usr/lib/libstdc++.so.6(_Znwm+0x34) [0x2b1d13841954]
> [deb64:03626] [ 9] /usr/lib/libstdc++.so.6(_Znam+0x9) [0x2b1d13841a49]
> [deb64:03626] [10] dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x33d)
> [0x44b9bd]
> [deb64:03626] [11] dock6.mpi(main+0x90a) [0x42cf6a]
> [deb64:03626] [12] /lib/libc.so.6(__libc_start_main+0xda) [0x2b1d13cc54ca]
> [deb64:03626] [13] dock6.mpi(__gxx_personality_v0+0xba) [0x41bf9a]
> [deb64:03626] *** End of error message ***
> mpirun noticed that job rank 0 with PID 3625 on node deb64 exited on signal 15
> (Terminated).
> 3 additional processes aborted (not shown).
>
>
> Should this attempt not follow what you had in mind, please suggest me what to
> modify and I'll do again.
> Thanks
> francesco
>
>
>
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
>
> > Hi,
> >
> > Ok, thanks for the updated report; we are keeping memory tuning
> > on our todo list.
> >
> > Here is an idea off the top of my head: try
> > grid_score_primary no
> > continuous_score_primary yes
> > This may trade cputime for memory.
> > Study the manual to keep the dock and grid settings consistent:
> > http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ContinuousScore
> >
> > If this works then there are definitely some easy cputime tunings
> > for continuous_score.
> >
> > Scott
> >
> > On Fri, 14 Mar 2008, Francesco Pietra wrote:
> >
> > > Forgot to add that with Dock6.1 I had also tried with a smaller box. Rigid
> > dock
> > > went on, while flex failed with the warning "could not complete growth;
> > confirm
> > > grid box is large enough to contain ligand and try increasing max_orients".
> > > Increasing max_orient was not a solution. In other words, I was faced by
> > either
> > > having too many points or a spatially inadequate room for my things. The
> > trial
> > > below with Dock 6.2 was for the large box and large sphere, 25A, which
> > embraces
> > > the whole molecular system.
> > >
> > > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > > > Date: Fri, 14 Mar 2008 02:30:58 -0700 (PDT)
> > >
> > > > The issue Orient: :match_ligand huge memory requirement (for large
> > ligands)
> > > > probably is not solved by DOCK v 6.2.
> > > >
> > > > I recall that with 106 CHO atoms, all scoring, including Amber rescore,
> > went
> > > > to
> > > > completion with DOCK v 6.1. In contrast, with same-family ligand of 118
> > CHO
> > > > atoms,the above issue arose already at the first stage of rigid dock. I
> > used
> > > > Andrew Magis' software for creating and selecting sphere, as the software
> > of
> > > > DOCK was unable to deal with so many points.
> > > >
> > > > I have tried now again with DOCK v 6.2 on the same machine (Debian Linux,
> > > > OpenMPI pointing to MPICH2, four cpu, 4GB memory per cpu, which, for
> > > > dual-opteron shared memory, means a total of 16GB ram available. Same
> > failure
> > > >
> > > > on
> > > >
> > > > mpirun -np 4 rigid.in rigid.out
> > > >
> > > > I add the input and screen outputs for documentation (and hopefully aid
> > in
> > > > circumventing the issue);
> > > >
> > > > RIGID.IN
> > > > ligand_atom_file /home/francesco/dockwork/ligand_dock62/lig_min43.mol2
> > > > limit_max_ligands no
> > > > skip_molecule no
> > > > read_mol_solvation no
> > > > calculate_rmsd no
> > > > orient_ligand yes
> > > > automated_matching yes
> > > > receptor_site_file
> > > > /home/francesco/dockwork/ligand_dock62/selected_spheres.sph
> > > > max_orientations 1000
> > > > critical_points no
> > > > chemical_matching no
> > > > use_ligand_spheres no
> > > > flexible_ligand no
> > > > bump_filter no
> > > > score_molecules yes
> > > > contact_score_primary no
> > > > contact_score_secondary no
> > > > grid_score_primary yes
> > > > grid_score_secondary no
> > > > grid_score_rep_rad_scale 1
> > > > grid_score_vdw_scale 1
> > > > grid_score_es_scale 1
> > > > grid_score_grid_prefix /home/francesco/dockwork/ligand_dock62/grid
> > > > dock3.5_score_secondary no
> > > > continuous_score_secondary no
> > > > gbsa_zou_score_secondary no
> > > > gbsa_hawkins_score_secondary no
> > > > amber_score_secondary no
> > > > minimize_ligand yes
> > > > simplex_max_iterations 1000
> > > > simplex_max_cycles 1
> > > > simplex_score_converge 0.1
> > > > simplex_cycle_converge 1.0
> > > > simplex_trans_step 1.0
> > > > simplex_rot_step 0.1
> > > > simplex_tors_step 10.0
> > > > simplex_final_min no
> > > > simplex_random_seed 0
> > > > atom_model all
> > > > vdw_defn_file /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> > > > flex_defn_file /usr/local/dock6/parameters/flex.defn
> > > > flex_drive_file /usr/local/dock6/parameters/flex_drive.tbl
> > > > ligand_outfile_prefix rigid
> > > > write_orientations no
> > > > num_scored_conformers_written 1
> > > > rank_ligands no
> > > >
> > > > SCREEN.OUT
> > > > Initializing MPI Routines...
> > > > Initializing MPI Routines...
> > > > Initializing MPI Routines...
> > > > Initializing MPI Routines...
> > > > terminate called after throwing an instance of 'std::bad_alloc'
> > > > what(): St9bad_alloc
> > > > [deb64:04547] *** Process received signal ***
> > > > [deb64:04547] Signal: Aborted (6)
> > > > [deb64:04547] Signal code: (-6)
> > > > [deb64:04547] [ 0] /lib/libpthread.so.0 [0x2b242c453410]
> > > > [deb64:04547] [ 1] /lib/libc.so.6(gsignal+0x3b) [0x2b242c58b07b]
> > > > [deb64:04547] [ 2] /lib/libc.so.6(abort+0x10e) [0x2b242c58c84e]
> > > > [deb64:04547] [ 3]
> > > >
> > /usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114)
> > > > [0x2b242c0f6424]
> > > > [deb64:04547] [ 4] /usr/lib/libstdc++.so.6 [0x2b242c0f45a6]
> > > > [deb64:04547] [ 5] /usr/lib/libstdc++.so.6 [0x2b242c0f45d3]
> > > > [deb64:04547] [ 6] /usr/lib/libstdc++.so.6 [0x2b242c0f46ba]
> > > > [deb64:04547] [ 7] dock6.mpi [0x42c654]
> > > > [deb64:04547] [ 8] /usr/lib/libstdc++.so.6(_Znwm+0x34) [0x2b242c0f4954]
> > > > [deb64:04547] [ 9] /usr/lib/libstdc++.so.6(_Znam+0x9) [0x2b242c0f4a49]
> > > > [deb64:04547] [10] dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x33d)
> > > > [0x44b9bd]
> > > > [deb64:04547] [11] dock6.mpi(main+0x90a) [0x42cf6a]
> > > > [deb64:04547] [12] /lib/libc.so.6(__libc_start_main+0xda)
> > [0x2b242c5784ca]
> > > > [deb64:04547] [13] dock6.mpi(__gxx_personality_v0+0xba) [0x41bf9a]
> > > > [deb64:04547] *** End of error message ***
> > > > mpirun noticed that job rank 0 with PID 4546 on node deb64 exited on
> > signal
> > > > 15
> > > > (Terminated).
> > > > 3 additional processes aborted (not shown)
> > > >
> > > > Thanks a lot for examining this report
> > > >
> > > > francesco pietra
> > > >
> > > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > > > > On Fri, 15 Feb 2008, Francesco Pietra wrote:
> > > > >
> > > > > > In order to plan my work, may I ask if Dock6.2 has reduced the memory
> > use
> > > > > of
> > > > > > Orient::match_ligand? If the answer is already implied in your last
> > few
> > > > > mails,
> > > > > > I beg pardon.
> > > > >
> > > > > Possibly, some memory related improvements have been made.
> > > > >
> > > > > Scott
> > > > >
> > > > > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > > > > >
> > > > > > > On Wed, 13 Feb 2008, Christian Schudoma wrote:
> > > > > > >
> > > > > > > > I am a PhD student in structural bioinformatics, trying to use
> > DOCK6
> > > > > for
> > > > > > > > docking ligands into RNA molecules, in particular riboswitches.
> > Are
> > > > the
> > > > >
> > > > > > > > DOCK6 scoring functions suitable for this task, i.e. have
> > NA-specific
> > > >
> > > > > > > > parameters been integrated into the latest DOCK version? In the
> > > > > > > > dockfans-archives I found a brief statement (Feb 2005) that
> > > > comparison
> > > > > > >
> > > > > >
> > > > >
> > > >
> > >
> >
> http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2005-February/000038.html
> > > > > > > > of "a variety of charge models for RNA" have been under way. Have
> > > > these
> > > > >
> > > > > > > > comparisons been fruitful? I wasn't able to find further or even
> > > > > > > > concluding information about this even after intensive research.
> > > > > > > >
> > > > > > > > If such modifications have not been made yet, does anyone have
> > > > > > > > experience with successfully docking to RNA targets and is
> > willing to
> > > >
> > > > > > > > share their parameters/scoring settings? Any help would be
> > > > appreciated!
> > > > > > > > (I already know about the article by Kang et al. (2003) =) )
> > > > > > >
> > > > > > > The test set used for "DOCK 6", which will be available after 6.2
> > > > > > > is released, is an RNA suite. And it includes some riboswitches.
> > > > > > > As far as RNA's, 6.1 is essentially the same as 6.2 except for
> > Amber
> > > > > score.
> > > > > > > There will be some new scripts to handle RNAs for Amber score.
> > > > > > > (In 6.1 and 6.0 the amberize scripts assume that an NA is a DNA.)
> > > > > > > 6.2 will be released very soon.
> > > > > > >
> >
> >
>
>
>
>
> ____________________________________________________________________________________
> Looking for last minute shopping deals?
> Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping
>
--
More information about the Dock-fans
mailing list