From: Ashar Malik (
Date: Wed Dec 24 2014 - 06:43:07 CST

> how can i calculate 1-4 vdW interaction energies for those atoms don't
> have 1-4 LJ parameters,

Three things:

1) You need to do some reading about what the force field terms are and
what do they actually mean?

2) What 1 - 4 means?

3) When you run a simulation/minimization energy terms are printed out to
the log file. vdW is a form of NONBONDED energy and has its own column. If
you want to do the calculation not on the entire system but a small
selection of atoms - look at ATOMSELECT to make the selection and use
NAMDENERGY to calculate the energy of your system.

Hope this helps.