Re: [AMBER] query about MD analysis

From: Clorice Reinhardt <>
Date: Tue, 10 Aug 2021 07:40:37 -0400

Hi Sadaf,

While these are generally good analyses to perform, I often find that it
helps to come into these types of problems with an objective or list of
things you are looking for AND consider if the timescale you are simulating
is appropriate for answering these questions.

Here are some general guidelines that may help you:

1) I imagine you are comparing WT and mutants and looking for differences.
However, how significant are differences between independent simulations of
mutants or wild-type?

2) Is 20 ns enough sampling? Remember, motions of side chains, larger scale
motions such as loops are on a longer time scale. Does your RMSD for both
the wild-type and ligand complex look stable?

Some people perform MMGBSA in these types of mutant/wt binding affinity
cases, and a really good strategy is to look for similar studies in the
literature and draw inspiration from the tools/types of analysis they do.
It sounds like you are on the right track, but framing some of your
questions and if the timescale/amount of sampling will be appropriate to
help you answer it will help.

All the best,


On Mon, Aug 9, 2021 at 8:42 PM Sadaf Rani <> wrote:

> Dear Amber users
> I run an MD simulation of wild-type and mutant protein-ligand complex for
> 20ns in amber and performed RMSD RMSF, Hydrogen bond analysis, SASA, Radius
> of Gyration, and SASA using cpptraj to access stability of the complex.
> What else analysis could I do to find the impact of ligand recognition or
> deleterious effect on its biological function? need your suggestions
> regarding analysis.
> Could you please give me any suggestions.
> Regards
> Sadaf
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Received on Tue Aug 10 2021 - 05:00:03 PDT
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