[Dock-fans] Ligand Docking with DOCK6
Francesco Pietra
chiendarret at yahoo.com
Fri Mar 14 02:30:58 PDT 2008
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.
> > >
>
>
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