On Sat, Oct 12, 2013 at 9:50 AM, Thomas Evangelidis <tevang3.gmail.com>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
> MMPBSA.py 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 MMPBSA.py. You can use the -deo
flag to dump out all decomp energies or you can use the MMPBSA.py 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Oct 12 2013 - 08:00:03 PDT
