[Dock-fans] parallel input script

Nancy Deng jdeng at adrik.bchs.uh.edu
Wed Jul 13 10:17:55 PDT 2005

Dear All,

I am seeking help from you about running dock on multiprocessors. I have  no 
problem now to let the database docking by 5.2 version on single node, 
(linux cluster).

The "dock.in" file was directly copied from the demo folder which is 
available in the 5.2 package. So, I added two lines to make it as the input 
for the parrallel script ( I also paste the dock.in below for your 
            parallel_jobs            yes
            multipleligands        yes

The problem is that after i lauched "dock5.mpi -i dock.in -o dock.out", the 
job was killed silently without any verbose complain. From the bottom of 
dock.out file, it shows
         " 0 Molecules Processed
            Elapsed time:   0.09 seconds"

I am just wondering whether anyone would suggest me how to solve the 
problem, and i'm very grateful to your any input!!!


**************below paste the input for your references********
ligand_atom_file                                             ./Peakdale.mol2
ligand_outfile_prefix                                        lig
limit_max_ligands                                            no
write_orientations                                           yes
write_conformations                                          no
initial_skip                                                 0
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no
rank_ligands                                                 no
num_scored_poses_written                                     1
orient_ligand                                                yes
automated_matching                                           yes
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
flexible_ligand                                              yes
ag_conf_search                                               yes
min_anchor_size                                              50
num_anchor_poses                                             50
number_confs_per_cycle                                       50
use_internal_energy                                          yes
internal_energy_att_exp                                      6
internal_energy_rep_exp                                      12
internal_energy_dielectric                                   4.0
use_clash_overlap                                            no
bump_filter                                                  yes
bump_grid_prefix                                             ../3_grid/grid
max_bumps                                                    3
score_molecules                                              yes
energy_score_primary                                         yes
energy_score_secondary                                       yes
vdw_scale                                                    1
es_scale                                                     1
nrg_grid_prefix                                              ../3_grid/grid
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
minimize_final_pose                                          yes
use_advanced_simplex_parameters                              no
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_anchor_min_max_iterations                            50
simplex_flex_min_max_iterations                              10
simplex_final_min_max_iterations                             100
simplex_random_seed                                          0
atom_model                                                   all
contact_score                                                no
parallel_jobs                                                yes
multiple_ligands                                             yes
***********end of dock.in attachment************

----- Original Message ----- 
From: "Sheng-Hung Wang" <gentamicin5 at yahoo.com.tw>
To: <dock-fans at docking.org>
Sent: Thursday, July 07, 2005 9:54 AM
Subject: Re: [Dock-fans] UCSF DOCK

> Try PMOL2Q, it's free.
> http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
> --- Shmuel Elmakies <shmulik at bioinfo.tau.ac.il>
>> Dear Sir/madam
>> I am new to DOCK 5. Reviewing the tutorial I noticed that the DOCK
>> procedure requires sybyl. This one is not mentioned in the
>> installation
>> section in the manual, and I was wondering whether it is mandatory or
>> can
>> be substituted by another package. how can I get it? Is it freeware?
>> Best Regards,
>> Shmuel Elmakies
>> System Administrator
>> Bioinformatics Unit
>> G.S. Wise faculty of Life Science
>> Tel Aviv University
>> Phone 972-3-6405099
>> _______________________________________________
>> Dock-fans mailing list
>> Dock-fans at docking.org
>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
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