[Dock-fans] DOCK amber_score terminated abruptly

Chinh Su Tran To chinh.sutranto at gmail.com
Mon Mar 25 21:55:38 PDT 2013


Hi Scott,

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 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?
*
*
Please help take a look. Thank you.

Chinh


*************************************** *
*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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