[Dock-fans] premature termination Amberscore

Teck Maan teck.m.lim at wmich.edu
Tue Jul 8 11:32:35 PDT 2008


Hi, 
I did with a -v flag. and the result is 
"
Initializing Library File Routines...
Initializing Amber_Score...

Reading the receptor input files.
Reading parm file (2hty.prmtop)
Error: unexpected EOF in 2hty.prmtop
Error: unexpected EOF in 2hty.prmtop"

Any idea where i have done wrong? I remove all the ions, ligands and
water. 

Thanks.
On Tue, 2008-07-08 at 12:38 -0700, Scott Brozell wrote:
> 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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