From: Ajasja Ljubetič (
Date: Mon Feb 06 2012 - 11:05:26 CST


Well since these are coordination "bonds" it might get a bit tricky. I see
two options (perhaps 3):
a) hope that interaction is mainly electrostatic (ionic) and that the
current non bonding parameters are good enough, so you don't have to do
b) Run a hybrid QM/MM simulation
c) decide that you don't want the calcium to leave the binding site and
lock the distances and orientation using additional bonds.

Best regards,

On Mon, Feb 6, 2012 at 17:37, Gurunath Katagi <>wrote:

> Dear all,
> I want to do a all atomic molecular dynamics simulation of a protein
> calbindin using NAMD with CHARMM (v27) (pbdid: 4ICB). in this protein,
> there is a link between Calcium ions and few protein atoms/water molecules.
> [These bonds are indicated by link section of the pdb file]
> but how do i add these links in proteins for simulations.
> what patches do i need to apply or are there any parameter files for these
> calcium-protein interactions.
> or deriving parameters for these bonds by using GAMESS/gaussian is the
> only option ..?
> please let me know ..
> Thank you
> Gurunath

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:11 CST