[Dock-fans] Fwd: Re: Ligand Docking with DOCK6
Francesco Pietra
chiendarret at yahoo.com
Fri Mar 14 02:43:29 PDT 2008
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
--- Francesco Pietra <chiendarret at yahoo.com> wrote:
> Date: Fri, 14 Mar 2008 02:30:58 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: [Dock-fans] Ligand Docking with DOCK6
> To: Scott Brozell <sbrozell at scripps.edu>
> CC: dock-fans at docking.org
>
> Hi Scott:
> 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:
>
> > Hi,
> >
> > 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.
> > > >
> >
> >
>
>
>
>
>
>
>
____________________________________________________________________________________
> Never miss a thing. Make Yahoo your home page.
> http://www.yahoo.com/r/hs
>
____________________________________________________________________________________
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