On Mon, May 4, 2015 at 2:06 PM, Ramin Ekhteiari <ramin_ekh.yahoo.com> wrote:
> Hi Dear Amber users,
> I would like to calculate delta free energy value between a ligand and its
> receptor, for this purpose I performed only one MD simulation for my
> complex (ligand + receptor) and then I submitted its trajectory frames
> into the MM_PBSA.py script to obtain binding free energy value, am I in a
> correct way? because in literatures I often saw that 3 MD simulations were
> needed for this kind of calculations (i.e, ligand, receptor and complex).
> I would be grateful for any advice from your site.
>
Both the single-trajectory and multiple-trajectory approaches are commonly
used in end-state free energy calculations (like MM/PBSA analyses). You
can see more details in the MMPBSA.py paper (
http://pubs.acs.org/doi/abs/10.1021/ct300418h) as well as a recent review (
http://onlinelibrary.wiley.com/doi/10.1002/minf.201100135/abstract
)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 04 2015 - 18:00:02 PDT
