[Dock-fans] DOCK amber_score terminated abruptly

Scott Brozell sbrozell at rci.rutgers.edu
Mon Mar 25 22:20:49 PDT 2013


Hi Chinh,

On Tue, Mar 26, 2013 at 12:55:38PM +0800, Chinh Su Tran To wrote:
> I checked the results which gave rec_lig_final_pose.pdb (but only for 1/100
> ligand conformations), somehow I guess the process might have done for the
> 1st ligand conformations, isnt it?

I do not understand the question.

> I ran with the verbose flag [-v], and below is what I got from the *dock.out
> *. This is one part of the file I took, and the rest of the file contains
> similar those lines of calculations. Does that mean the calculation of
> complex energy is not completed? Otherwise, I did not find any other
> errors, but just 1 warning in the "*amberize_complex.lig.out" *saying *"the
> unperturbed charge of the unit: 6.000400 is not zero". *Is this the point
> that caused the problem?

A small nonzero unperturbed charge is innocuous.
The dock.out below looks fine.  This is for the first ligand.
You should examine the verbose output and files for the ligand being
processed when the termination occurred.
If there are no errors or warnings in the amberize files or the dock
output for that ligand (and be sure to visualize the coordinates for
that ligand) then the most likely causes are resource exhaustion.
What happens if you run with only one ligand, namely the one 
being processed when the termination occurred.

scott

> *************************************** *
> *Computing the complex energy:*
> *
> *
> *Minimization reached the maximum number of iterations.*
> *The random number is 1454538876*
> *Minimization reached the maximum number of iterations.*
> *Done computing the complex energy.*
> *
> *
> *
> *
> *Energy of the complex rec_noH.lig_contact_conformers100.1 is
> -5854.28451647    *
> *Energy of the receptor rec_noH is -5755.07373593    *
> *Energy of the ligand lig_contact_conformers100.1 is -92.2159391818    *
> *
> *
> *
> *
> *Reading the ligand lig_contact_conformers100.1 input files.*
> *
> *
> *Number of ligand strands is 1*
> *Number of ligand residues is 1*
> *Number of ligand atoms is 76*
> *
> *
> *Reading the complex rec_noH.lig_contact_conformers100.1 input files.*
> *Number of complex strands is 3*
> *Number of complex residues is 199*
> *Number of complex atoms is 3210*
> *
> *
> *************************************** *
> *Computing the ligand energy:*
> *
> *
> *Minimization reached the maximum number of iterations.*
> *The random number is 1454538876*
> *Minimization reached the maximum number of iterations.*
> *Done computing the ligand energy.*
> *
> *
> *
> *
> *************************************** *
> *Computing the complex energy:*
> *
> *
> * -124.41      0.00    -42.86  1.45e+01*
> *ff:  74    -50.97    111.78      4.52   -124.37      0.00    -42.90
>  1.66e+01*
> *ff:  75    -50.39    112.37      4.47   -124.16      0.00    -43.06
>  1.75e+01*
> *ff:  76    -54.20    108.63      4.32   -123.86      0.00    -43.29
>  1.65e+01*
> *ff:  77    -59.48    103.47      4.16   -123.58      0.00    -43.53
>  1.44e+01*
> *ff:  78    -61.71    101.46      3.93   -123.39      0.00    -43.70
>  1.33e+01*
> *ff:  79    -59.40    104.00      3.68   -123.33      0.00    -43.75
>  1.43e+01*
> *ff:  80    -55.42    108.22      3.39   -123.38      0.00    -43.65
>  1.57e+01*
> *md:          80      0.080      35.29     -55.42     -20.13     155.79*
> *ff:  81    -53.36    110.47      3.08   -123.53      0.00    -43.38
>  1.63e+01*
> *ff:  82    -53.88    110.15      2.76   -123.69      0.00    -43.11
>  1.59e+01*
> *ff:  83    -54.51    109.72      2.46   -123.83      0.00    -42.87
>  1.56e+01*
> *ff:  84    -52.68    111.76      2.17   -123.87      0.00    -42.74
>  1.65e+01*
> *ff:  85    -49.55    115.13      1.88   -123.84      0.00    -42.71
>  1.79e+01*
> *ff:  86    -48.65    116.31      1.63   -123.79      0.00    -42.80
>  1.85e+01*
> *ff:  87    -51.85    113.38      1.44   -123.73      0.00    -42.95
>  1.77e+01*
> *ff:  88    -57.38    108.16      1.36   -123.75      0.00    -43.15
>  1.58e+01*
> *ff:  89    -61.16    104.68      1.38   -123.88      0.00    -43.33
>  1.44e+01*
> *ff:  90    -60.86    105.18      1.52   -124.15      0.00    -43.41
>  1.47e+01*
> *md:          90      0.090      41.54     -60.86     -19.32     183.38*
> *ff:  91    -58.21    107.89      1.77   -124.50      0.00    -43.37
>  1.59e+01*
> *ff:  92    -56.43    109.58      2.10   -124.84      0.00    -43.26
>  1.66e+01*
> *ff:  93    -57.03    108.69      2.46   -125.12      0.00    -43.06
>  1.62e+01*
> *ff:  94    -58.15    107.17      2.80   -125.24      0.00    -42.87
>  1.56e+01*
> *ff:  95    -57.50    107.34      3.06   -125.17      0.00    -42.73
>  1.57e+01*
> *ff:  96    -54.50    109.88      3.25   -124.95      0.00    -42.68
>  1.68e+01*
> *ff:  97    -51.89    112.11      3.38   -124.63      0.00    -42.74
>  1.75e+01*
> *ff:  98    -52.43    111.29      3.47   -124.31      0.00    -42.88
>  1.71e+01*
> *ff:  99    -55.11    108.41      3.51   -124.04      0.00    -42.99
>  1.60e+01*
> *ff: 100    -56.56    106.85      3.53   -123.92      0.00    -43.02
>  1.58e+01*
> *md:         100      0.100      38.64     -56.56     -17.92     170.57*
> 
> 
> 
> 
> 
> 
> On Tue, Mar 26, 2013 at 3:02 AM, Scott Brozell <sbrozell at rci.rutgers.edu>wrote:
> 
> > Hi Chinh,
> >
> > Depending on the outputs of interest to you,
> > you can continue the Amber score run; for example, you could
> > prune all the already calculated and attempted conformations from
> > the input .mol2 file.  However, that would affect the contents of
> > the outputed .mol2 files.
> >
> > The best practice is to determine the cause of the failure.
> > Have you inspected the Dock Amber score files produced during preparation ?
> > This link gives advice:
> >
> > http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AmberScorePreparationScripts
> > Note that this is the most likely source of error.
> >
> > Have you inspected the Dock Amber score output ?
> > If there are no clues here, such as error or warning messages, then
> > try running with the verbose flag, -v.
> >
> > scott
> >
> > On Mon, Mar 25, 2013 at 07:04:57PM +0800, Chinh Su Tran To wrote:
> > > I was running DOCK for calculating amber_scores for 100 conformations
> > > results from DOCK_contact_score. The process was fine, *no error*, but it
> > > was terminated abruptly.
> > > The results contain 3 files, 2 out of which (i.e. conformers.mol2 and
> > > ranked.mol2) are empty. That's obvious because the process was
> > unfinished.
> > > I guess that's memory involved or kind of. Am I wrong? Please correct me.
> > >
> > > My question is only that if it is possible to continue the
> > DOCK_amber_score
> > > run with what it left off as we can do with MD. I checked the
> > > *dock.out*and it shows a lot of values (around more than 112,000
> > > lines) and
> > > incomplete.
> > > Please show me how to continue the run if it is applicable.


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