AMBER Archive (2002)

Subject: Re: non-bonded metal ion in complex

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Tue Sep 17 2002 - 08:59:14 CDT

I would recommend applying distance restraints on the O-Mg bonds
instead of position restraints. Dealing with metal ions is always
tricky.

I am not sure you can easily tackle this problem by manual editing of
the prmtop file.

--- yuann <yuann_at_bioinfo.ndhu.edu.tw> wrote:
> Greetings all,
> I now get trouble with dealing with a non-bonded metal ion in a
> complex
> before running sander. This complex forms with two identical organic
> molecules and a magnesium ion which is near two O(-). (R-O- [Mg2+]
> -O-R)
> Initial structure was taken from PDB. I'm worried that magnesium ion
> will
> act as a free ion during energy minimization/MD due to no suitable
> parameter for this condition. Can I solve this problem by applying a
> harmonic restrain with force constant(eg. 100K ) or edit prmtop file
> of
> this molecule to become a residue instead of three residues? (I
> remember
> this skill is mentioned in DNA Tutorial, but have no idea what to do
> in
> this case.)
> Any comment will be appreciated.
>
> Best Regards,
> sychen.
>
>
>

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