Pair interaction energy

From: Sundaramoorthy, Munirathinam (m.sundaramoorthy_at_Vanderbilt.Edu)
Date: Fri Jan 30 2004 - 10:46:22 CST

Dear NAMD users,

I like to calculate the interaction energy of a heterodimeric protein
complex. I do know the residues in both chains that are at the
interface. Is this enough to input these residues in
"pairInteractionFile" for the interaction energy calculations?


Alternatively, is it good enough if I calculate energies of individual
chains (A & B) and the dimer (AB) and use the difference [(A+B)-AB] as
the interaction energy?




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