[Dock-fans] inv_a error

Scott Brozell sbrozell at rci.rutgers.edu
Mon Jan 23 23:50:41 PST 2012


On Thu, Jan 19, 2012 at 10:50:15AM +0100, Jose R. Valverde wrote:
> 	I am running a dock job using Zou GB/SA scoring, and I keep getting
> a number of errors in each pose calculation, all of the kind
> 	Pure ligand inv_a error: 46     -20.749
> 	Receptor on ligand inv_a error: 33      -24.7508
> 	I suspect this means the calculation results will be wrong and 
> should not be used. Right? Or is this just an informative message that
> can be disregarded?

After reading section 2.2 of
this error indicates that the sum in eqs 21 and 22 has grown so big
that the multiplicative inverse of the Born radius of the atom,
1/alpha_i in the paper, aka gb_lig_inv_a[i] in the code, will be
negative.  To avoid this unphysical situation, the code assigns 0.1
to gb_lig_inv_a[i].

You should examine atoms 46 of the ligand and 33 of the receptor.
Perhaps there is a simple explanation and a simple fix.

good luck,

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