[Dock-fans] premature termination Amberscore

Scott Brozell sbrozell at scripps.edu
Tue Jul 8 12:57:40 PDT 2008


Hi,

On Tue, 8 Jul 2008, Teck Maan wrote:

> 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. 

No, except a general failure in preparation.

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
Did you:
In particular, examine the amberize*.out and *.log files for warnings and errors. Experience using AMBER will help in understanding and judging the impact of the messages in these files. Correcting problems may involve substantial effort. See the DOCK Fans mailing list for specific examples.

Did you view your receptor in a graphics program: 2hty.prmtop

Scott

> 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
> > > 



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