VMD-L Mailing List

From: Bahaa Mostafa (bmostafa_at_sci.cu.edu.eg)
Date: Wed Dec 24 2014 - 02:54:43 CST

hi,
as a part of my PhD thesis, i'm working on a script to calculate energy
using a charmm force field for small molecules, strictly CGenFF, but i feel
no good upon extracting 1-4 LJ parameters,

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 ?

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

could you tell me how to do so or recommend a reference discuss this point
explicitly,

thanks in advance, 

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