I understand that the old Mg2+ parameters are not the greatest and that in general divalent ions are problematic in a force field. In that sense it is understandable that it does just work, but at the same time when they are some of the only parameters available that is what people are going to use - hopefully knowing the inherent risks/challenges, and if not someone will hopefully question that in peer-review..
I am looking at other Mg parameters to use as well, like the Oelschlaeger et al. from 2007 in JMB. Any others that people come across would be greatly appreciated.
Best regards,
Jesper
On Jan 18, 2012, at 12:19 PM, David A Case wrote:
> On Wed, Jan 18, 2012, Jesper Sørensen wrote:
>>
>> Is this not a bug still though? Not that I mind changing the source
>> code/parameter files at all, but shouldn't this work automatically.
>
> As the archive states, there are no *Amber* parameters for magnesium; this
> fix allows you to use some very old parameters, which can at least get you
> started in the right direction, and which might be enough for problems that
> don't depend strongly on what the magnesium is doing (e.g. if it is just
> staying in one place and neutralizing negative charge.)
>
> The next release will (probably) include this fix. I'm personally nervous
> that people will expect Mg2+ to "just work"....
>
> ...dac
>
>
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Received on Wed Jan 18 2012 - 13:00:02 PST
