From: Marcos Sotomayor (
Date: Thu Feb 23 2012 - 16:44:47 CST

Hi Gurunath

On Wed, 22 Feb 2012, Gurunath Katagi wrote:

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

Was your protein simulated in a water box? I've done multiple simulations
of proteins with bound calcium ions and never seen them flying away with
the standard CHARMM force-field (and a system that included a water box
surrounding the protein).

I've seen reports of flying calcium ions in simulations performed in
vacuum though. You may want to also keep the crystallographic water
molecules that are nicely coordinating the Calcium in your structure.


>> 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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