Re: [AMBER] Selection of forcefield for protein-ligand simulations

From: Carlos Simmerling <>
Date: Thu, 25 Mar 2021 15:49:54 -0400

an important aspect of successful simulations is the choice of an
appropriate compromise between speed and accuracy. it's hard to make
general statements about ligand binding studies, but my personal opinion is
that many of the ligand differences that people might want to explore tend
to have differences of a small number of atoms. Such differences can be
hard to model without including atomic detail. Also, since most ligand
binding studies do not aim to sample large conformational changes, speed is
not as important as accuracy. Of course there are times when speed is a
higher priority, such as in the study of ligand binding pathways, or when
ligand binding or dissociation leads to a large conformational change in
the protein. In those cases, the best choice may be to forego atomic detail
in terms of longer simulations. At the other extreme, QM/MM studies where
the ligand is treated with QM may be best for short simulations that are
highly accurate for modeling things like enzymatic reactions.
the details (and the model with the ideal compromise) depend on what
timescale you need to sample, and how important it is that you model the
ligand with high accuracy.

On Thu, Mar 25, 2021 at 3:22 PM Prasanth G, Research Scholar <> wrote:

> Dear all,
> I would like to know your opinion about the choice of forcefields (all-atom
> vs united atom) for running protein-ligand simulations. From the literature
> search, I understood that majority of the protein-ligand simulations make
> use of an all-atom forcefield.
> I would be grateful if you could provide some references that could help me
> understand the reason behind this choice.
> Thank you in advance.
> Regards,
> Prasanth G.
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Received on Thu Mar 25 2021 - 13:00:02 PDT
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