From: Aron Broom (
Date: Mon Feb 06 2012 - 12:09:08 CST

Is this calcium binding critical to what you are studying? If so I think
you probably need to do the guassian stuff. You could look at just
refitting the charges with existing bond parameters using the RED server (, as it doesn't sound like there are
fully covalent bonds here, but the electrostatic parameters will probably
not be sufficient without refitting.

If it's not critical, and you just want the calcium to stay there, maybe
what Ajasja says in c)


On Mon, Feb 6, 2012 at 12:05 PM, Ajasja Ljubetič

> Hi,
> 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
> anything.
> 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,
> Ajasja
> 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

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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