Re: gurukatagi@gmail.com

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Feb 22 2012 - 11:51:51 CST

>
> >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<http://www.ks.uiuc.edu/Research/namd/2.8/ug/node55.html#SECTION0001322120000000000000>
(defined
between the Ca and the coordinating atoms) and lock it to the desired value
using harmonic restraints<http://www.ks.uiuc.edu/Research/namd/2.8/ug/node56.html#SECTION000133700000000000000>.
This is probably simpler, it it works.

Best regards,
Ajasja

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