AMBER Archive (2004)

Subject: AMBER: 1-4 EEL

From: tang kwa (
Date: Tue Dec 07 2004 - 11:12:54 CST

Dear all,

I finished my simulation which is the organic molecule
in the water box. By now I would like to calculate the
binding energy of solute and solvent. I extracted the
coordinate from the trajectory and then calculated the
energy by using sander. I used this equation :

Ebinding = E(mol + Wat ) - E (mol) -E(Wat)

The E (mol) is calculated in gas phase. Form the
results I got very difference 1-4 Electrostatic

           mol+Wat mol Wat
1-4 EEl -40 -230 0

EEl -11747 70 -11707

1-4VDW 12 12 0


I don't understand the why I got difference value in
1-4 EEl. Can I evaluate the interation as I told you?

Thank you in advance.


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