Re: [AMBER] Metal Ion Model

From: Carlos Modenutti <cpmode.gmail.com>
Date: Fri, 30 Oct 2015 16:06:42 -0300

Hi Pengfei,
nobonded works very well.
Thanks!
Regards
Carlos

2015-10-23 16:28 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:

> 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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>
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Received on Fri Oct 30 2015 - 12:30:05 PDT
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