From: Aron Broom (
Date: Wed Feb 22 2012 - 12:08:08 CST

If you really don't care that much about what the calcium does to the
protein dynamics, then maybe just lock it in place with a harmonic

If you think this calcium will be important for dynamics, you should search
for AMBER tutorials that deal with having amino acids bound to metal ions.
In these cases a non-standard residue is made that has a covalent linkage
to the metal ion, and the partial charge parameters for all the residues
that will bind that metal are refit using the R.E.D. Server. This is
important if you want an accurate effect, as having a +2 charge sitting
next to your amino acids will dramatically alter their partial charge
characteristics and could have a big effect on the dynamics in that region.

On Wed, Feb 22, 2012 at 12:51 PM, Ajasja Ljubetič <
> wrote:

> >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 ..?
>> No, I mean that you change the force field parameters to
> define additional covalent bonds between the Ca and the atoms to which the
> Ca is coordinated.
> This is probably quite a bit of work, since you have to estimate the
> bond constants and angle bending constants. (Or just set them to high
> numbers to have the Ca bound rigidly)
> I also have another idea: perhaps you could use the colvar coordNum<> (defined
> between the Ca and the coordinating atoms) and lock it to the desired value
> using harmonic restraints<>.
> This is probably simpler, it it works.
> Best regards,
> Ajasja

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

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