bipin singh wrote:
Hello,
I am willing to study the free energy of binding of a cation (Ca++) to
the protein and I am following the free energy tutorial
provided by Justin
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy
).
Please let me know whether the settings for this type of study would
be same as given in the tutorial for ligand-Protein
binding free energy calculation or it need some different approach:
By decoupling a Ca2+ ion, you are removing 2 charges from the system. I don't
know how to properly treat such a case (perhaps someone else can comment), but
likely you'll find such topics in the literature. A better approach may be
umbrella sampling, but again the literature should point you to reasonable
methodology. I'm sure others have dealt with such questions before.
-Justin
The setting from the ligand-Protein binding free energy calculation
are given as:
van der Waals coupling:
sc-alpha = 0.5 ; use soft-core for LJ (de)coupling
sc-sigma = 0.3
sc-power = 1
couple-moltype = LIG
couple-intramol = no
couple-lambda0 = none ; non-interacting dummy in state A
couple-lambda1 = vdw ; only vdW terms on in state B
Coulombic coupling:
sc-alpha = 0 ; soft-core during (dis)charging can
be unstable!
sc-sigma = 0
couple-moltype = LIG
couple-intramol = no
couple-lambda0 = vdw ; only vdW terms in state A (the
previous state B is now A)
couple-lambda1 = vdw-q ; all nonbonded interactions are on in state B
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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