I agree with Christina, which is not hard because she knows these things
better than I do.
I am just want to share our experience. Every time we thought ourselves
clever and tried not to use Mg2+ with ADP/ATP, the phosphates go out of
their way to find ANYTHING positively charged, and find lysines and
arginines very quickly, giving the wrong result.
adrian
On 2/21/19 10:01 AM, Christina Bergonzo wrote:
> Hello,
>
> Without knowing specifics about your system, I would guess that ignoring
> the contribution of Mg2+ to chelating ADP would be bad in general, and also
> not representative of the system you want to simulate.
> Mg2+ is parameterized in Amber, you can check the Amber manual, page 51 to
> read more about the ion parameters available.
>
> Good luck!
> -Christina
>
> On Tue, Feb 19, 2019 at 1:57 PM Antonio Amber Carlesso <
> antonio.amber.carlesso.gmail.com> wrote:
>
>> Hi all,
>>
>> We are interested in performing a MD simulations of a protein where on its
>> kinase active is co-crystallized ADP and Mg2+
>>
>>
>>
>> Is there any general rule when we would like to simulate a system with a
>> divalent cation (in this case Mg2+) in its pocket site?
>>
>>
>> A simplistic approach could be remove the ion before simulations.
>>
>> When this "simplistic approach" could be considered a bias in the analysis?
>>
>> Any considerations/reflections about it?
>>
>>
>>
>> Thank you!
>> _______________________________________________
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>>
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Feb 21 2019 - 12:00:02 PST
