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
>>>
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>>
>>
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>
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Received on Thu May 17 2012 - 13:00:02 PDT
