Hi Carlos,
Will you expect to see the ligand switching of the Ca2+ center? If not, you can use the bonded model. If yes, (and also due to Ca2+ usually don’t have much strong binding with the surrounding residues), I would recommend you to use the nonbonded model or cationic dummy atom model. Amber has nonbonded model parameters for Ca2+ available and the nonbonded model is easier to set up than the cationic dummy atom model. So I would suggest you try the nonbonded one first.
Best,
Pengfei
> On Oct 22, 2015, at 6:42 PM, Carlos Modenutti <cpmode.gmail.com> wrote:
>
> Dear Amber user group
> I need to carry out a molecular dynamics simulation of a protein
> carbohydrate complex but, in the carbohydrate binding site are two calcium
> ions (in direct contact with ligand). Which is the better ion metal model
> for this situation? (bonded, nonbonded or cationic dummy atom model)
> Best regards
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Received on Fri Oct 23 2015 - 12:30:04 PDT
