[Dock-fans] Unknown Close Contact Warning
sbrozell at rci.rutgers.edu
Thu Sep 23 00:27:33 PDT 2010
On Tue, Sep 14, 2010 at 11:36:53AM -0400, Fuhrman, Kit wrote:
> I'm re-scoring my compounds with the Amber score. Some of my ligands display an error in the amberize_ligand log
> "Warning: Close contact of 0.618328 angstroms between .R<<0> 1>.A<H24 37> and .R<<0> 1>.A<H28 44>"
> The problem is that when I measure the distance between the atoms, H24 and H28, the distance is not even close to .618328. In this case it's 0.786114712. This happens for quite a number of ligands. When I view the mol2 in chimera or pymol, I can't find anything terribly wrong with the molecules. If I ignore the errors, I get a reasonable amber score.
> I've attached the ligand. Has anyone seen this before? Any suggestions on how to zero in on the cause?
The close contact reported is actually the square of the distance:
sqrt(0.618328) = 0.786
At the very least the warning should be clearer, but this may be a
legacy issue within Amber. I'll investigate.
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