From: Ashar Malik (
Date: Thu Dec 25 2014 - 00:03:08 CST

> but i don't use NAMD, i can't install it on my PC (windows) at all,

NAMD doesn't have to be installed on windows. You download it. Unzip the
folder and from the dos prompt use NAMD just like you would use it in

> i have VMD installed correctly, but i don't know if it calculates energy
> with charmm force field,

There are ways of connecting VMD with NAMD to run simulations and stuff.

> so i have to do calculations myself,

What does this mean? How are you doing it yourself?

> my question again :
> some atoms have 1-4 LJ parameters , but others don't have,
> what does it mean ?
> does it mean these atoms have no vdW interaction?,
> or does it mean i should use the not 1-4 LJ parameters instead of these
> missing parts ?

All the information required to do MM calculations is present in the force
field files, unless you are working with unique atoms. You should use NAMD
rather than using this alternative method which makes you believe that
something is missing from the force field.