Dear Jesper,
not, we did not try. I am in general, if possible,
trying to avoid divalents in NA simulations, since
their basic force field form is not very realistic
due to lack of charge transfer and polarization.
I.e., there is problem with the basic LennardJones+pointcharge
approximation, which definitely is not a real Mg2+ ion.
It is not clear to me how to design a proper test.
I think, Tom may comment on that, usual problem
with the "standard" parameters has been formation of undesired
inner-shell binding
contacts during equilibration even when not intended.
On the other hand, in ribosome and ribozymes, there
are inner-shell Mg2+ interactions, although the
experimental uncertainties are also very substantial....
So I would tell inclusion of Mg2+ into NA simulations
is a difficult issue where we have selection of several
bad options.
Jiri
>
> Dear Jiri,
>
> Have you tried them out already?
> Okay, well I am not using them for RNA just yet, but I might sometime later.
>
> I still have to run some production simulations with them before I will comment on their quality.
> But I think the situation is more a result of a lack of magnesium parameters to pick from. Here is what I have found:
>
> Single atom parameters:
> * Charmm27 (developed by B. Roux, no publication of the development)
> * Amber9x (developed by J. Aqvist 1990)
> * Allner et al. enhancement of the B. Roux parameters for Charmm (2012)
>
> Dummy atom models (MD62+):
> * Oelschlaeger et al. (2007)
> * Sept and co-workers (maybe 2012)
>
> I like the idea of the dummy atom models, but I've tried the Oelschlaeger and they don't return correct ion-water rdfs (in pure water) and I see some things when I use it with proteins, where the octhedral coordination is not great, and waters are replaced by direct-interaction with the protein (this latter thing may not be incorrect). Also, they were not developed for TIP* water models or the AMBER MD setup. Plus they change some parameters in the amberFF when they performed their publications.
> The Sept and co-worker parameters are not freely available yet, but hopefully will be sometime soon.
>
> So for now it will be the single atom parameters I will use and newly developed parameters that match experimental results, seem like a better choice than parameters from 1990. Not saying that older parameters aren't sometimes better than newer ones - it depends on the property you are investigating I guess. That is just my 2 cents...
>
> All the best,
> Jesper
>
>
> On May 17, 2012, at 12:19 PM, Jiri Sponer wrote:
>
> > 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
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 17 2012 - 13:00:03 PDT
