[Dock-fans] DOCK amber_score terminated abruptly

Scott Brozell sbrozell at rci.rutgers.edu
Mon Mar 25 12:02:36 PDT 2013

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:
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.


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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