Ion-protein and protein-protein interactions

From: Vishal Kopardé (vnk_sim_at_yahoo.co.uk)
Date: Thu Oct 26 2006 - 12:50:48 CDT

Hi All,
        I am new to NAMD and to protein simulations. I am trying to run a
NPT simulation of a protein-ion complex in aqueous solution, a Zn ion
stabilized protein hexamer in water. Do I need to specify any monomer-
monomer and/or Zn-monomer interactions? or the vdw and electrostatic
interactions will take care of them. In such simulations, where the
protein has a well-defined tertiary structure (in this case hexamer)
do I need to fix the backbone or restrain the CA atoms to maintain
the tertiary structure? or will the structure be maintained with any
special constraints because it is more energetically favorable?
        Thank you,
Vishal
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