[Dock-fans] Fatal error about amber score.

Äî Áõ yolanda.only at yahoo.com.cn
Sat Apr 12 20:48:00 PDT 2008


Dear dock-fans:
   
  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
------------------------------------------------------------------------------------------
  Initializing Library File Routines...
   
  I really appreciated for any answers.
   
  Best regards,
   


Yolanda Guo
Northeast Normal University   

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