[Dock-fans] Dock6.2 installation - possible failures judgment
sbrozell at scripps.edu
Tue Apr 1 00:18:20 PDT 2008
On Wed, 26 Mar 2008, Ben Keshet wrote:
> Thanks for looking at my test output. The first file is indeed
> 'secondary2_conformers.mol2.dif' as you corrected. Where the
> differences are significant, as in
> 'primary_secondary_score/secondary7.dockout.dif, you wrote that you
> think that these difference are likely due to the grids being generated
> on different machines. Do you think that this is only a "scaling"
> difference? That is, do you think that overall - docking positions and
> ranks, would generally be qualitatively similar across different machines?
> I visually inspected 'secondary7_secondary_conformers.mol2' and the
> original 'secondary7_secondary_conformers.mol2' as well as the
> 'secondary7_secondary_scored.mol2' files (using Chimera) and they look
> different, although some conformers look alike (not the best one).
> On a related note - the same possible failures occurred when I installed
> dock6.1 a while ago. I ran part of the test_suite available online
> (first 23 structures), which is validated for dock5.4, with dock6.1.
> The rigid scores were off by ~5 and the flexible by ~2. The rmsd of the
> scored ligands from the 'ligand.mol2' structure in each set of
> receptor-ligand are 2-3 angstrom with only one docked ligand being
> completely off.
> Taken together, it looks to me like despite these failure my machine
> docked the test_suite successfully for the most part. If you have any
> other measures I could use to validate the installation and performance
> of dock on my machine I'd be happy to use them.
Not really; I notice this
Parallel Processing Test Set
> Scott Brozell wrote:
> > Hi,
> > On Mon, 17 Mar 2008, Ben Keshet wrote:
> >> I installed Dock6.2 and have several 'possible failures' after running
> >> 'make test'. I inspected the output of 'make check' and most failures
> >> were insignificant differences in tails of floating point. However,
> >> differences in the scores in secondary_conformers.dif and
> >> secondary_scores.dif(2,4, and 7) seem more significant. secondary7
> >> (primary + secondary with minimization) has huge differences in the grid
> >> and contact scores.
> >> Some of the .dif files are pasted below. I am running dock on a PC with
> >> cygwin. I would greatly appreciate if anyone experienced users could
> >> help me in judging the severity of these failures or suggest how to fix
> >> them.
> >> ./primary_secondary_score/secondary2_secondary_conformers.mol2.dif
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