[gmx-users] Bug in g_rms -> calculate RhoSc ??

[K.A. Feenstra]

Marc Baaden wrote:
> Hi,
> 
> I was trying to use the alternative similarity measures Rho
> and Rho Scaled from the Crippen and Maiorov paper. Rho looks
> fine, but Rho scaled doesn't make sense, in the way that it
> even looks like a bug to me ..

I haven't yet looked at your examples, but I was the one that implemented
the rho/rho_sc measures in g_rms. I've definitely fixed some bugs before
I was satisfied, and have checked several peptide conformations visually
to see whether the calculated figures made any sense in comparison with
the 'visual overlap' of the structures. Also, the behavior corresponds
qualitatively to the description in the Crippen & Maiorov paper.

Other than that, there is no straightforward way of rigorously testing
it, since I don't have reference structures to test against. Perhaps
I (we?) could contact (one of) the authors to ask for a few structures
with known rho/rho_sc differences. Do feel free, in the meantime, to
check my implementation against the formulae in the paper. I did do
some re-writing to get a more straightforward implementation.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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