[Dock-fans] Fatal error about amber score.

Scott Brozell sbrozell at scripps.edu
Tue Apr 15 09:48:37 PDT 2008


Hi,

How big are the ligands and the receptor ?
What are the total and available memory ?

One possibility is to increase your available resources:
Some machines have a very
restrictive policy on allocating available resources:
increase the datasize, stacksize, and memoryuse
using the limit, ulimit, or unlimit commands;
for many Linuxes this command sequence will work:
limit; unlimit; limit
Otherwise read the man pages or apply trial and error
to find the apt use of these commands.

Another possibilty is to 
rank_ligands                                                 no
but this probably won't save much space.

Divide and conquer will work.  Split your calculation into two runs.

Scott

On Sat, 12 Apr 2008, Äî Áõ wrote:

>   I have installed dock6.2 and run the amber score, but it still has the same problem. When it calculated 214 compouds, it stoped and displayed the warning that was:
>   FATAL: allocation failure in ivector <>
>   My total compound is 300. Are my compounds too much?
>   I did the amber score making every parameters default.
>   I run dock in windows XP by cygwin. The content of the output file named dock.out is as follows: 
>    
>   --------------------------------------
> DOCK v6.2
>   Released March 2008
> Copyright UCSF
> --------------------------------------
>   
> Molecule Library Input Parameters
> ------------------------------------------------------------------------------------------
> ligand_atom_file                                             D:\yolanda\new_dock\specs\druglike1\amber\amber1_1\druglike1_1.amber_score.mol2
> limit_max_ligands                                              no
> skip_molecule                                                   no
> read_mol_solvation                                            no
> calculate_rmsd                                                  no
>   Orient Ligand Parameters
> ------------------------------------------------------------------------------------------
> orient_ligand                                                no
>   Flexible Ligand Parameters
> ------------------------------------------------------------------------------------------
> flexible_ligand                                              no
>   Bump Filter Parameters
> ------------------------------------------------------------------------------------------
> bump_filter                                                  no
>   Master Score Parameters
> ------------------------------------------------------------------------------------------
> score_molecules                                              yes
>   Contact Score Parameters
> ------------------------------------------------------------------------------------------
> contact_score_primary                                        no
> contact_score_secondary                                      no
>   Grid Score Parameters
> ------------------------------------------------------------------------------------------
> grid_score_primary                                           no
> grid_score_secondary                                         no
>   Dock3.5 Score Parameters
> ------------------------------------------------------------------------------------------
> dock3.5_score_primary                                        no
> dock3.5_score_secondary                                      no
>   Continuous Energy Score Parameters
> ------------------------------------------------------------------------------------------
> continuous_score_primary                                     no
> continuous_score_secondary                                   no
>   Zou GB/SA Score Parameters
> ------------------------------------------------------------------------------------------
> gbsa_zou_score_primary                                       no
> gbsa_zou_score_secondary                                     no
>   Hawkins GB/SA Score Parameters
> ------------------------------------------------------------------------------------------
> gbsa_hawkins_score_primary                                   no
> gbsa_hawkins_score_secondary                                 no
>   Amber Score Parameters
> ------------------------------------------------------------------------------------------
> amber_score_primary                                            yes
> amber_score_secondary                                         no
> amber_score_receptor_file_prefix                             protein_rec
> amber_score_movable_region                                   ligand
> WARNING:  No parameter value found for "amber_score_minimization_rmsgrad".  Default value of "0.01" used.
> amber_score_before_md_minimization_cycles                    100
> amber_score_md_steps                                          3000
> amber_score_after_md_minimization_cycles                     100
> amber_score_gb_model                                          5
> amber_score_nonbonded_cutoff                                 18.0
> amber_score_temperature                                       300.0
> WARNING:  No parameter value found for "amber_score_abort_on_unprepped_ligand".  Default value of "yes" used.
>   Warning:  No secondary scoring function selected.
>   
> Molecule Library Output Parameters
> ------------------------------------------------------------------------------------------
> ligand_outfile_prefix                                        druglike1_1
> write_orientations                                           no
> WARNING:  No parameter value found for "num_scored_conformers".  Default value of "1" used.
> rank_ligands                                                 yes
> max_ranked_ligands                                           500
> ------------------------------------------------------------------------------------------



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