On 20/01/11 10:53, Brian Smith wrote:
> Just checked back through old versions of the CNS/XPLOR forcefield and it
> has always been so. I guess this is partly historical - NMR structures
> were typically recorded at lower pH if they could be - and partly a good
> default setting as electrostatics didn't used to be used for refinement.
>
> Even if you set a different (partial?) protonation state in analysis, I
> would be surprised if ARIA paid attention to what you'd done if the
> residue code was still HIS in the sequence though. Looks as if the data
> model is intended to deal with protonation state via "chain state"s rather
> than alternative residue types.
>
> If you know that your HIS are likely to be singly protonated (experimental
> evidence, pH, etc.) and can either determine or want to take a punt on
> which N is protonated then you should use the HISD or HISE patches in your
> ARIA setup.
>
> I reckon that you are right that it would be nice to be able to set your
> experimental pH, per residue pKas, and have CNS/ARIA cope with that,
> because as you say it will likely have an impact on the water refinement
> stage. Probably not a high priority in the grand scheme of things though!
>
> Brian Smith
>
Hi Brian,
it might be historical, but this doesn't make it correct.
In my case I defined an hbond to a NE2 of a HIS which doesn't work if is
protonated. The donor proton and HE2 just clash.
Thanks for pointing to the HIS-patches in Aria. I never payed attantion
to it. Am I correct, HISD means proton on ND1 and HISE means prton on HE2 ?
Justin
--
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117
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