[Dock-fans] Unknown Close Contact Warning

Fuhrman, Kit kit.fuhrman at pathology.ufl.edu
Tue Sep 14 08:36:53 PDT 2010

Dear Dockfans,

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?
Is it just an artifact?

Best regards,

Kit Fuhrman
IDP Graduate Student
Department of Pathology, Immunology and Laboratory Medicine
University of Florida College of Medicine
kit.fuhrman at pathology.ufl.edu

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