[Dock-fans] premature termination Amberscore

Scott Brozell sbrozell at scripps.edu
Tue Jul 8 12:38:20 PDT 2008


Hi,

Rerun it with the the verbose output flag: -v

Scott

On Tue, 8 Jul 2008, Teck Maan wrote:

> I was running amber for the protein 2HTY on a molecule that i created.
> However, it stopped prematurely at "Initializing Library File
> Routines..." Is there a size limitation for the protein molecules?
> Thanks in advance.
> 
> Teck Maan
> 
> 
> 
> --------------------------------------
> DOCK v6.2
> 
> Released March 2008
> Copyright UCSF
> --------------------------------------
> 
> 
> Molecule Library Input Parameters
> ------------------------------------------------------------------------------------------
> ligand_atom_file
> lig.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                             2hty
> amber_score_movable_region                                   ligand
> amber_score_minimization_rmsgrad                             0.01
> 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
> amber_score_abort_on_unprepped_ligand                        yes
> 
> Warning:  No secondary scoring function selected.
> 
> 
> Molecule Library Output Parameters
> ------------------------------------------------------------------------------------------
> ligand_outfile_prefix                                        output
> write_orientations                                           no
> num_scored_conformers                                        1
> rank_ligands                                                 no
> ------------------------------------------------------------------------------------------
> 
> Initializing Library File Routines...
> 



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