Re: [AMBER] tMD and free energy calculation

From: Bill Ross <>
Date: Mon, 9 Sep 2019 02:03:58 -0700

A basic tenet is that you can only compare energies of the same exact
molecule in molecular mechanical force fields. However, I suspect you
can compare the energy difference of two conformations of one molecule
to two conformations of a similar one, but lack the theory to convince
the betting scientist. Here I'm talking just about total internal
energies of static conformations, which I suspect rarely satisfy real
needs, and I don't know if there's even a convenient path to that, in
spite of years on my part wondering about it. :-) Energy of interaction
with the environment in an ensemble of states is beyond my pay grade.

For static, internal energies, you could extract files of just the loop
in question from the saved coord files, creating .rst files to match a
prmtop you'd create for the loop, and run a step of minimization in
vacuum to get energies, all in a script. Maybe something less tedious is
available now; there used to be an energy analysis prog.


On 9/9/19 1:38 AM, Elena Gomez wrote:
> Hi,
> I performed a tMD to study the opening of a loop in two similar proteins (wild type and mutant). In the tMD of the mutant the opening does not occur, and I need to calculate the energy difference between open and closed conformation for both proteins to explain it, how can I do it?
> Thank you.
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Received on Mon Sep 09 2019 - 02:30:02 PDT
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