[Dock-fans] negatively charged sulfonamides

[John J. Irwin]

Hi Eric

Thanks for looking at this issue.

Eric Pettersen wrote:
> Hi all,
> The issue was raised recently about problems with Chimera's treatment
> of metal-coordinating sulfonamides.  It's been decided to treat such
> an amide as NH-.  It's been proposed that this may be hard to deal
> with in some docking scoring methods because of the ionization energy.
>  The question is how much of an issue is it?  If it was a big deal
> then I could provide an option to treat the amide as NH2 instead.  Of
> course, I don't want to write the code to handle the option unless I
> really need to!
I think there needs to be an amidate atom type, for both primary and
secondary sulfonamides.  R'(R'')NH -> R'(R"")[N-] and R'NH2 -> R'[NH-]. 
What I don't know is to what extent this can be handled by existing
code/options/atom types.

I can drop by to chat if that would help.

John


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