[AMBER] Help to choose best-fit ion model

From: anu chandra <anu80125.gmail.com>
Date: Fri, 29 Jan 2016 14:26:39 +0000

Hello Amber users,

The protein I am working with have a Mn2+ ion at its active site. The ion
suspected to form coordination bond with neighboring residues and these
bonds will break and re-form during the course of reaction. As read from
the tutorial page, I suppose I should use the non-bonded model. But, after
going through the description of bonded and non-bonded models in the
tutorial page, I am a little confused about the model I should choose. The
tutorial says about the bonded model that -

' While ligand exchange of coordination number (CN) switching process
certainly do happen in protein metal sites, these occur on much slower
timescales than what is observed for metal ions in aqueous solution.
.......... Since typical MD simulation timescales are at the nanosecond or
microsecond levels (circa 2014), the bonded model is an effective approach
to study processes where ligand exchange does not occur over the timescales

Though the Mn2+ ion in my protein do suggested to have CN switching during
the catalysis, I am aiming for only about 100ns simulation to find out the
role of some water molecules in the ligand-ion interaction. So I just
wonder which model will be best fit in my case.

Any suggestions would be very much appreciated.
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Received on Fri Jan 29 2016 - 06:30:03 PST
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