On 9/19/12 11:47 AM, 이종화 wrote:
Greetings all,
I am trying to compare the stability of two protein-ligand systems where
ligands differ. I am trying to observe the difference of interaction energy
between the ligands. Would it be correct to make energy groups of Protein,
Solvent, Ligand, and compare the energy obtainable by g_energy? I am
confused because in one tutorial I do also have to run simulation with only
the ligand and solvents.
You can certainly measure interaction energy in this way, though there are
probably more robust methods like LIE and free energy calculations.
If it were to be correct, would comparing the sum of the LJ-14:Protein-LIG
and Coul-14:Protein-LIG of each ligand be okay?
Neither of those terms will be of any use, and should actually be zero. 1-4
interactions are intramolecular. What you're likely more interested in are the
LJ-SR and Coul-SR terms, though there are still some flaws with doing that,
especially if using PME. This topic is discussed frequently on the mailing
list; the archive should provide many useful discussions on such topics.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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