From: Gurunath Katagi (
Date: Wed Feb 22 2012 - 11:22:01 CST

On Mon, Feb 6, 2012 at 10:35 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.

but when i simulate with those parameters, the calcium ions are flying (i.e
are not at stable,), which is not desirable ...

> 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.

 do u mean to say that , show i fix these calcium atoms using "fixedatoms"
options [setting Bfactor column to 1] or apply tclforces to control the
distances and orientations ..?

Its not calcium binding that we are interested , but the dynamics of the
proteins ..
Kindly let me know ..

Thank you

> 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

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