[Dock-fans] premature termination Amberscore

Teck Maan teck.m.lim at wmich.edu
Tue Jul 8 10:40:24 PDT 2008


Hi,
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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