[MMTK] How to assign different forcefield parameter to the same kind of atoms

[Konrad Hinsen]

On 07.01.2004, at 03:55, Takefumi SORA wrote:

> For example, some "CA"-"CA" bond length is 1.4A,
> other "CA"-"CA" bond length is 1f etc.
> In the same way, I want to change bond_K parameter,
> angle paramter etc.
>
> Does anybody know how to do this ?
>
There are three possible solutions I can think of:

1) Create a new atom type whose parameters are identical to CA except 
for the CA-CA bond stretching potentials.  This is easy in principle, 
but a bit of an effort to realize, as you have to make sure that each 
potential term involving CA is copied, and also because you have to 
define interactions between standard CA and your modified CA.

2) Leave the potential as it is, and define an additional potential 
that subtracts out the CA-CA interactions that you want to modify, and 
then adds the new terms. You could use the module 
MMTK.ForceFields.Restraints for that.

3) Define your own subclass of the AmberForceField that assigns 
different parameters to selected CA-CA terms.

Konrad.