Re: [AMBER] silver parameters

From: Christina Bergonzo <cbergonzo.gmail.com>
Date: Fri, 12 Apr 2019 09:48:50 -0400

Hi,

Having looked into this briefly, I can tell you that it's most likely going
to be difficult at best.
Each silver-mediated base pair in DNA has a different net charge, so you
would have to parameterize the base-Ag-base with MCPB (I think):
http://ambermd.org/tutorials/advanced/tutorial20/index.htm
Maybe you can figure out a way to have Ag ions with more than one oxidation
state, i.e. rename some ions AG1 AG2 etc. and protonate/deprotonate your
bases as needed, and let any NMR restraints take care of the rest.

This paper might be helpful (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773525/) - it uses a QM/MM
approach that you could also try.

Good luck!
-Christina

On Fri, Apr 12, 2019 at 9:29 AM UroŇ° Javornik <Uros.Javornik.ki.si> wrote:

> Dear people of the Amber community,
>
> I have a question about running an NMR refinment on a nucleic acid -
> silver system. In the system I have silver ions bound within DNA base pairs
> in place of some of the usual hydrogens. What is a sensible approach to
> this problem? Can I define new, deprotonated residues and make a non-nonded
> model, or should a bonded model be used? In the latter case, are
> appropriate parameters for the silver ion in this environment already
> available somewhere, or do I have to develop new parameters?
>
> Best regards,
> UroŇ°
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


-- 
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Fri Apr 12 2019 - 07:00:02 PDT
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