Dear Jesper, Tom:
it still does not predict perfmormance in RNA simulations,
which may be a specific issue, so difficult to tell if they
are to be recommendd.
Jiri
> Thanks Tom. I'll probably submit these to the "Bryce" parameter database one of the following days. I have talked to the author about this.
>
> One way I checked to see if my implementation was correct was to run a single point energy in NAMD of an Mg-Mg system in the gas-phase.
> I did this using the parameters in charmm (which they were developed for) and in amber (with the files I attached).
>
> I then checked for a variety of distances that the energies I got were the same (I was both in the repulsive and attractive regions).
>
> I redid the above procedure using the older Roux parameters in charmm as well, just to check that that worked too.
>
> Does that sound like a reasonable test?
>
> Best,
> Jesper
>
> On May 16, 2012, at 12:03 PM, Thomas Cheatham III wrote:
>
> >
> >> I have recently been working on this and I am still in the testing phase, but these files (attached) should make it possible to use
> >> the Allner et al. parameters you are referring to.
> >
> > I haven't tried these new parameters for Mg2+ yet (but we plan too),
> > however the approach proposed in the Allner et al. paper to get decent
> > association times for the Mg2+ ions is clever and compelling. I am fairly
> > confident that these will be better than the current default AMBER-adapted
> > Aqvist Mg2+ parameters (where we have observed funny artifacts in DNA
> > simulation such as ions tunneling into the helix leading to base pair
> > disruption). Jesper's attachments look correct.
> >
> > --tec3
> >
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>
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Received on Thu May 17 2012 - 12:30:03 PDT
