[Dock-fans] when dock6.mpi crashes....

[Scott Brozell]

Hi,

On Wed, 3 Oct 2007, Francis E Reyes wrote:

> How about writing conformers for all molecules that were ranked?
> 
> Are those now lost?

Yes, previously ranked conformers are lost.

If one has a large library or an unstable computing environment
then one should consider printing out individual conformations
on the fly.  See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
Once all the calculations have completed then concatenate the output
files and run a follow up calculation that merely ranks the poses
without redocking or rescoring them.

Scott

> On Oct 3, 2007, at 9:31 AM, Scott Brozell wrote:
> 
> > On Tue, 2 Oct 2007, Francis E Reyes wrote:
> >
> >> What steps can I do to restart where it left off? I understand I
> >> could use skip_molecule, but how about ranking, writing out  
> >> conformers?
> >
> > There is no restart facility yet; see these for past comments:
> > http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-August/ 
> > 001164.html
> > http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-October/ 
> > 000750.html
> >
> > Scott