Re: Free energy calculations

From: Pratik Narain Srivastava (
Date: Mon Aug 30 2021 - 09:08:56 CDT

Look for the Cafe plugin for VMD to use MMPBSA. there is also a new binding
free energy estimator in the alpha versions of the latest VMD but it is not
MMPBSA based.

On Mon, 30 Aug, 2021, 7:32 pm Nancy Singh, <> wrote:

> Hii,
> I have done simulations for my protein-ligand complex for 20ns. Now I want
> to calculate the binding free energy for my ligand and protein. I am new to
> using In NAMD so I don't have any idea how to approach it. In AMBER we can
> use for free energy calculation that I know.
> What is the alternative for this in NAMD? It will be really helpful if I
> can get any insight on this.
> Thank you
> Regards,
> Nancy

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