[gmx-users] Fwd: geometry optimization of metalloenzyme

[Justin Lemkul]

On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote:
> Hello everyone,
>
> I am trying to minimize the potential energy of a
> metalloenzyme containing Ni and Fe atoms.
> What is the best way to constrain (fix?) the position of the active site
> atoms
> during the geometry optimization?
> I have tried introducing bonds with relatively high force constants and
> alternatively, tried introducing a [constraints] section,
> but the atoms are still not staying put.

Bonds or constraints will maintain distances between atoms (relative 
position) but not absolute position.

> Or should one use extra position restraints?

If the absolute position matters, yes. I would think the approach of 
adding restraints or constraints between atoms would be more meaningful 
given that preserving coordination geometry is often the defect in MM 
treatment of transition metals.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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