Re: ABF Questions

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sat Jul 21 2018 - 06:03:39 CDT

On Sat, 21 Jul 2018 at 04:17, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Two questions about ABF:
>
>
> 1) Right now I have the center of mass of my ligand as the main atoms and
> the center of mass of my protein as the ref atoms (i.e. all of the CA C N O
> atom types of the backbone). But if for my ref atoms I just the center of
> mass of one of the side chains near the middle of the protein, could this
> change my PMF results drastically? How critical is the choice of ref atoms
> within the protein for ABF with a ligand in the protein?
>

That is actually a question about your protein, not about ABF.

> (Is there a limit of atom numbers that can be used for the ref atoms?)
>
There is no limit. Large numbers will incur a performance penalty, but a
few dozens or even a couple hundred should be fine - especially with a
center-of-mass-based coordinate.

> 2) The lowerboundarywall and upperboundarywall are used essentially to
> keep say a ligand within the specified window, but how much does the choice
> of value itself have an effect on the PMF result? Would 10 kcal/mol vs 100
> kcal/mol for these values have a large effect on my results?
>

Most likely not. The only case that could be a problem is a PMF that is
steeply decreasing towards the boundary, but it is more typically
increasing.

Jerome

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