Re: [AMBER] MD Simulation of chemical complex

From: David Case <>
Date: Thu, 25 May 2017 10:31:59 -0700

On Mon, May 22, 2017, ruqaiya khalil wrote:
> I have NMR data of interaction between two compounds to form a complex
> (three proposed models). Now, I want to perform MD Simulation of the system
> to identify the most stable model.

You can certainly run simulations on three proposed models. It is not certain
that existing force fields will enable you to find the most stable model,
however. Details matter a lot, here, and it is quite common to have alternate
conformations that cannot be distinguished in an energetic sense with most
MD simulaitons.

That said, people in the NMR field (and, indeed, in other fields) do this
sort of thing all the time, picking the structures with the lowest energies
to describe and deposit to databases.


AMBER mailing list
Received on Thu May 25 2017 - 11:00:03 PDT
Custom Search