Re: [AMBER] umbrella sampling protein

From: David A Case <>
Date: Tue, 22 Sep 2020 11:22:11 -0400

On Tue, Sep 22, 2020, Ramin Mehrani wrote:
>I am trying to do an umbrella sampling simulation with amber to calculate
>the dimerization free energy of protein with more than 200 residues. The
>major part of this calculation is to apply a harmonic restraint to the
>distance between two proteins chain. The harmonic restraint will keep the
>distance fluctuating around a target distance with tunable amplitude.

>According to this tutorial, to apply the harmonic restraint to the distance
>we need to define the center of mass of two groups of atoms via "igr1 and
>igr2". The problem with this method is that we cannot group more than 200
>atoms. I was wondering if you know a method in amber that I can apply the
>harmonic restraint to the distance between two groups with more than 200
>atoms. I am asking this because each protein chain in my study has more
>than 200 atoms.

Simplest approach is to choose a subset of atoms, say the CA atoms in
residues in regular secondary structure. Use the center of mass of
those atoms as a surrogate for the COM of the whole protein.

I'm not sure if the "nfe" collective variables let you define groups
with an arbitrary number of atoms or not. You might look into that
options as well (Section 23.4 in the Reference Manual.)


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Received on Tue Sep 22 2020 - 08:30:02 PDT
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