Re: Binding free energy analysis at specific time interval during MD trajectory

From: Pratik Narain Srivastava (
Date: Thu Jul 08 2021 - 14:56:13 CDT

I assume you plan to do MMPBSA for binding free energy calculation. You can
use the Cafe plugin for VMD. It requires a dcd file with your required
number of frames and the psf file. So the starting pose of your ligand
really shouldn't matter.

You can also calculate non bonding interaction energies using the namd
energy plugin. The documentation is self explanatory and very simple to

On Fri, 9 Jul, 2021, 12:20 am Mi Yang, <> wrote:

> Dear Colleagues,
> In one of our papers, we have run MD simulations for 60 ns. The RMSDs were
> found reasonable stable but one reviewer asked to see what is the
> difference of Binding Energy among original seeded (best docked) structure
> and at some time intervals eg. at 20 ns or 30ns etc.
> We have successfully extracted frames at different time intervals but
> really have no idea how to calculate binding free energy for a frame
> without changing specific docked structure?
> We docked protein-ligand with autodock vina, prepared MD input with VMD
> and ran through NAMD.
> Any helpful suggestions will be highly encouraging?
> Best Regards,
> Dr. Shabbir

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