From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
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.
On Mon, Feb 6, 2012 at 17:37, Gurunath Katagi <gurunath.katagi_at_gmail.com>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
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