[Dock-fans] Fwd: Re: Ligand Docking with DOCK6
Francesco Pietra
chiendarret at yahoo.com
Sat Mar 22 08:45:50 PDT 2008
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.
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
The screen output was the same as on the failed rigid dock using grid:
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.
> > > > > >
>
>
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