[Dock-fans] Fwd: Re: Ligand Docking with DOCK6
Scott Brozell
sbrozell at scripps.edu
Fri Mar 14 18:47:51 PDT 2008
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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