Because I am only interested in the non-bonded
interactions for the ion Zn and Ca , the only parameters
I need to add to the force field are th r, epsilon and
charge. Does someone tell me how to do that? I try to edit
the frcmod.pcy with only Mass and NONBON parameters and then
"loadamberparams", after that the zinc and Ca were still
not recognized while loading the pdb file.
And how to add the charge of ions?
Every residue that is loaded into leap must be defined in order for
the atoms to be recognized. See the tutorials for examples of defining
residues - for ions, the residue is a single atom. Also, in
amber6/dat/leap/lib I believe you'll find scripts for generating some
ion residues.
Defining a residue involves defining the atom types (which must
correspond to the type names in the frcmod) and the atom charges.
Bill Ross
Received on Wed Oct 24 2001 - 17:04:58 PDT
