[Dock-fans] How to continue when terminated unexpectedly

[Scott Brozell]

Hi,

On Thu, 30 Aug 2007, gongxingwen wrote:

> Hi, I would like to know if I can continue the previous work (flex or amber dock) when it was terminated unexpectedly such as power failure. Any parameter has this function ? Thanks! Gong

There is still no special restart option yet:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-February/000577.html

Generally, one examines the output files to determine what has
been calculated and then modifies the new inputs accordingly.

For Amber rescoring, only with the verbose option, dock6 -v ...,
does dock emit enough information to in general determine what
poses have been rescored.  In particular, in the output
...
ligand_atom_file        FINAL_new_AM1BCC_conformers.amber_score.mol2
...
Reading the ligand FINAL_new_AM1BCC_conformers.2 input files.
...

The 2 is the AMBER_SCORE_ID.  This is determined from the order of the
pose in the mol2 file argument to prepare_amber.pl.
So in principle one could merely count the number of rescored ligands
to determine where to trim the ligand_atom_file input; however,
this requires careful attention to detail.  In the next release we shall
improve the AMBER_SCORE_ID handling.

Scott