Subject: MPI dock5.1

From: anna ferrari <[email-masked]>
Date: Wed, 13 Nov 2002 11:35:22 +0100

Hi
I'm running an MPI dock 5.1.0 on a linux machine but I have some problems.

If I run the job on a _single processor_ with the following _input file_

---------------------------------------
ligand_atom_file                 xtal-lig.mol2
ligand_outfile_prefix          xtal-lig-3n
write_orientations                 yes
write_conformations            yes
calculate_rmsd                      yes
rank_ligands                           no
max_send_queue_size            10
max_recv_queue_size            10000
orient_ligand                         yes
automated_matching             yes
receptor_site_file                 spheres_use
max_orientations                 1000
flexible_ligand                     no
bump_filter                         yes
bump_grid_prefix               ../rec_linux
max_bumps                         3
score_molecules                  yes
contact_score_primary          no
contact_score_secondary        no
energy_score_primary           yes
energy_score_secondary         yes
vdw_scale                             1
es_scale                                 1
nrg_grid_prefix                ../rec_linux
minimize_ligand                yes
minimze_rigid_anchor           yes
minimze_layer_growth           yes
minimze_final_pose                 yes
minimze_final_pose_rigid         no
minimze_final_pose_torsions    no
minimize_final_pose_complete   yes
minimizer_choice                        0
initial_translation                     1.0
initial_rotation                          1.0
initial_torsion                          10.0
maximum_iterations                100
maximum_function_calls         100000
window_based_termination       no
scaled_range_termination          no
multiple_simplex_cycles           no
random_number_generator        0
random_number_seed             2002
atom_model                     all
vdw_defn_file                  vdw.defn
flex_defn_file                 flex.defn
flex_drive_file                flex_drive.tbl
calc_internal_energy           no
max_ranked_ligands             100
scored_mol_output_override     yes
gbsa_score_secondary           no
---------------------------------------

* dock doesn't process any molecule writing this _output file_*

---------------------------------------
DOCK v5.1.0

Released 10-15-2002
Copyright UCSF
Authored by:
        Tack Kuntz
        Demetri Moustakas
        Scott Pegg
        Fernando Martin
--------------------------------------

Molecule Library Parameters
------------------------------------------------------------------------------------------
ligand_atom_file               pm_prova.mol2
ligand_outfile_prefix          pm_prova
write_orientations             no
write_conformations            no
calculate_rmsd                 no
rank_ligands                   yes
max_ranked_ligands             100
scored_mol_output_override     yes
max_send_queue_size            20
max_recv_queue_size            1000

Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                  yes
automated_matching             no
distance_tolerence             0.3
distance_minimum               0.5
nodes_minimum                  3
nodes_maximum                  4
receptor_site_file             spheres_use
max_orientations               1000

Anchor & Grow Parameters
------------------------------------------------------------------------------------------
flexible_ligand                no

Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                    yes
bump_grid_prefix               ../rec_linux

Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                yes

Contact Score Paramters
------------------------------------------------------------------------------------------
contact_score_primary          no
contact_score_secondary        no

Energy Score Parameters
------------------------------------------------------------------------------------------
energy_score_primary           yes
energy_score_secondary         no
vdw_scale                      1
es_scale                       1
nrg_grid_prefix                ../rec_linux

GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_score_secondary           no

Warning:  No secondary scoring function selected.  Primary scoring 
function will be used as secondary.

General Optimization Parameters
--------------------------------------------------------------------------------
minimize_ligand                yes
minimze_rigid_anchor           no
minimze_layer_growth           no
minimze_final_pose             yes
minimze_final_pose_rigid       no
minimze_final_pose_torsions    no
minimize_final_pose_complete   yes
minimizer_choice               0

Simplex Optimization Parameters
-------------------------------------------------------------------------------
initial_translation            1.0
initial_rotation               1.0
initial_torsion                10.0
maximum_iterations             100
maximum_function_calls         500
window_based_termination       no
scaled_range_termination       no
multiple_simplex_cycles        no

Random Number Generation Parameters
-------------------------------------------------------------------------------
random_number_generator        0
random_number_seed             2002

Molecule Parameters
------------------------------------------------------------------------------------------
atom_model                     all
vdw_defn_file                  vdw.defn.old
flex_defn_file                 flex.defn
flex_drive_file                flex_drive.tbl
calc_internal_energy           no
------------------------------------------------------------------------------------------

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Bump Filter Routines...
 Reading the bump grid from ../rec_linux.bmp
Initializing Energy Score Routines...
 Reading the energy grid from ../rec_linux.nrg

*0 Molecules Processed*

-Running an MPI job using _four processors_ and the same input file, 
this is the final message:

*0 Molecules Processed
WARNING assign_vdw_labels: No vdw parameters for 1  C3
p3_11707:  p4_error: interrupt SIGSEGV: 11
*
after writing four times the input parameters.

My command line is a dock.com file
---------------------------------
#!/bin/tcsh
#PBS -l nodes=1:ppn=1,walltime=48:00:00

cd /home/giulio/anna/search
mpirun -np 1 -machinefile $PBS_NODEFILE 
/home/giulio/dock5/dock_5.1.0/bin/dock5.linux -i dock.in > dock.out
---------------------------------------------------------------------------------------

Any suggestion?

Thank you in advance
Anna