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:
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
--
-----------------------
Regards,
Bipin Singh
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