[Dock-fans] parallel input script

Terry Lang terry at cgl.ucsf.edu
Mon Jul 18 18:08:19 PDT 2005


Dear Nancy,

In order to run dock using multiple processors, you need to use the
following commands:

 % set path = ( $path /usr/local/mpi/bin )

 % mpirun -np 8 dock5.mpi -i dock.in -o dock.out


This should take care of your mpi problem. However, if mpi was the
problem for your run, you would get different output. Try running the
multi-ligand mol2 file again without mpi to see if there is something
additionally wrong.

Good luck,
Terry


Nancy Deng wrote:

> 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 reference):
> 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!!!
>
> nancy
>
> **************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
> receptor_site_file ./selected_spheres.sph
> 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
> vdw_defn_file /usr/usc/dock/5.2.0/parameters/vdw_AMBER_parm96.defn
> flex_defn_file /usr/usc/dock/5.2.0/parameters/flex.defn
> flex_drive_file /usr/usc/dock/5.2.0/parameters/flex_drive.tbl
> chem_defn_file /usr/usc/dock/5.2.0/parameters/chem.defn
> 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
>>>
>>
>>
>> __________________________________________________
>> ·Q§Y®É¦¬¨ì·s«H³qª¾¡H
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>
>
> _______________________________________________
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-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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