Hi John,
not sure if this is helpful as a starting point, but an analysis of common methods for geometry optimisations in periodic boundary conditions, incl. a comparison with a crystal structure and free R-factors, has been published in
J. Phys Chem B 2014, 118, 14612-14626. Therein you can also find a literature review and a summary of the work by Ryde and Thiel in the area of quantum refinement of protein X-ray structures with QM/MM.
Best wishes,
Lars
Dr Lars Goerigk | Lecturer & ARC DECRA FellowSchool of Chemistry | The University of MelbourneVictoria 3010 | AustraliaWebsite: goerigk.chemistry.unimelb.edu.auFollow me on Twitter: https://twitter.com/lgoer_compchem
On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35.-$-.gmail.com <owner-chemistry-$-ccl.net> wrote:
> Ignoring hardware and software demands for the moment is it preferable/practical/wise to optimize such a structure?It depends on whether it is intrinsically disordered or not. It also depends on whether you want an in vivo representation or if you think the in-vacuo representation is representative of the actual structure in vivo.Jim
To: Kress, Jim <jimkress35]![gmail.com>
Subject: CCL: Protein structuresFolks,
I realize that over time development of technology may have an impact on reliability or accuracy of protein XRAY structures. How does one determine accuracy or reliability of such structures? Ignoring hardware and software demands for the moment is it preferable/practical/wise to optimize such a structure?
Many thanks!
John
--John McKelvey
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