On Mon, May 13, 2013, dilrajl.bii.a-star.edu.sg wrote:
> I am trying to calculate the free energy of a
> protein-peptide system using mmpbsa.py script from Amber12.
>
> The "DELTA TOTAL" value for the complex and ligand doesn't look
> correct to me. The energy values are positive and the standard
> deviations are huge.
Look at the individual snapshot numbers that go into computing the final
averages; I suggest starting with the ligand. Are there a few outliers
(leading to a large std. deviation)? Look at the structures of snapshots that
have widely different reported energies. This will be the beginning of a
debugging process you need to follow to see why the results are the way they
are.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 13 2013 - 05:00:02 PDT
