How to parametrize new atom types in Namd

From: Dian Jiao (
Date: Fri Jan 17 2014 - 15:44:50 CST

I want to simulation a series of metal ions in water. However, only a
few ions have parameters in namd(charmm). What do I do to get
parameters for new atom type, e.g. Rb? When I looked at
par_all27_prot_lipidNBFIX.prm, metals only seem to have LJ parameters,
for example:
ZN 0.000000 -0.250000 1.090000 ! ALLOW ION

Is that all you need for metal ions? Where does it specify atomic
charge, etc. Or am I missing something?


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