Re: [AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands?

From: Carlos Simmerling <>
Date: Tue, 17 Mar 2020 06:18:53 -0400

I'm not sure that it's clear what to do. The model is heavily empirically
adjusted, and I would expect that the same kind of adjustments need to be
made to any other components that you add. The functional form is
compatible I believe, so toy can always try mixing things out of the box,
but until people report results we don't really know.
It's not so much that it isn't ff14SB, it's that the vdw parameters were
changed, and things were empirically adjusted for a specific solvent model
and so on.... It was optimized as a single unit and how much that will
suffer by introducing components from a different source is uncertain.

On Tue, Mar 17, 2020, 4:24 AM Homeo Morphism <>

> I'm about to start using force field a99SB-disp for proteins. For a
> description of what it is, see here:
> Now, what if I study membrane-bound receptors that interact with synthetic
> ligands. Normally, we use force fields lipid17 and gaff2. But I assume
> they've been developed with the idea that ff14SB would be used for
> proteins. Now that I'm switching to a99SB-disp, how would I go about
> parameterizing lipids and ligands? How safe would it be to use lipid17 and
> gaff2?
> Any ideas are most welcome.
> Thanks.
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Received on Tue Mar 17 2020 - 03:30:02 PDT
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