Just my two cents:
Simply modelling divalent metal ions and point charges with a Lennard-Jones
potential is notoriously difficult. I would say (and this is perhaps big
leap) that the loose consensus in the literature is that the parameter
space available to such a model is generally not adequate to reproduce all
of the desired (bulk) quantities, although balancing the errors between
them is certainly possible.
The main point here is that one needs to think about what types of behavior
one wants to investigate and then perhaps augment the model as appropriate.
More complicated alternative models also exist (the recent 12-6-4
potentials in AMBER14) and may be worth considering.
Regards,
Brian
On Thu, Jul 31, 2014 at 10:07 AM, Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hello,
>
> There are Co2+ ion parameters provided with Amber14.
> They are in the $AMBERHOME/dat/leap/parm directory, and are from the paper
> below:
> http://pubs.acs.org/doi/abs/10.1021/ct400146w
>
> Other Co2+ parameters also exist and are discussed in the above paper.
>
> -Christina
>
>
> On Thu, Jul 31, 2014 at 7:58 AM, Jinfeng Huang <wwsshhjjff00.163.com>
> wrote:
>
> > Dear Amber Users,
> >
> >
> > I am simulating a protein with Co2+ at the active site. I have tried to
> > search for the parameters that someone have released, but I found
> nothing.
> > Herein, I hope you can provide me a strategy to solve the problem.
> > Any help is greatly appreciated. Thank you!
> >
> > Jingfeng Huang
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> 30 South 2000 East, Rm. 201
> Salt Lake City, UT 84112-5820
> Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652 / Fax: (801) 585-6208
>
> ---------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
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Received on Thu Jul 31 2014 - 07:30:03 PDT
