Re: [AMBER] running on an NMR ensemble

From: Jason Swails <>
Date: Sat, 12 Oct 2013 10:51:25 -0400

On Sat, Oct 12, 2013 at 9:50 AM, Thomas Evangelidis <>wrote:

> Greetings,
> I am wondering if there is any straight forward way to get the per-residue
> free energy decomposition from an NMR ensemble in pdb format. I know
> can be run with a single frame, but in my case I guess I must
> solvate and equilibrate each frame of the NMR ensemble by imposing
> holonomic constraints to the protein dimer, and then concatenate to create
> an input trajectory. Is this correct?

PDB files with an NMR ensemble are typically separated into MODELs. Do you
have a topology file for a single structure? If so, you can actually use
the PDB file as the input trajectory for You can use the -deo
flag to dump out all decomp energies or you can use the API to
load the data into a dict-like object and perform your own analyses
directly in Python. Just use the PDB file where you would normally put the
NetCDF or ASCII trajectory file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Oct 12 2013 - 08:00:03 PDT
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