[gmx-users] Value for bonded force constant (Kb)

[raja]

Hi Gmxions,

The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance
(type6, Harmonic potential) between Fe(II) and corresponding ligating
atoms N and O (of amino acids) at the end of 5000 steps of energy
minimization. That is newly introduced Kb value is able to restraint at
around 2-3 A (Which is the average value found from crystal structure)
when comparing to more than 5A in the absence of Kb value.

I am going to start MD with a hope that this success will also be there
at the end of 2ns simulation
 Is there any second thought? 

With thanks!
B.Nataraj


On Wed, 10 May 2006 05:16:26 -0700, "raja" <raja_28 at fastmail.us> said:
> Hi Mr Tsjerkw,   
> Thanks for your mail. Infact I intented to attach
> the reference link but I missed it. Anyway here is the link where I
> taken
> the value of Kb. Infact the reference only talk between Fe and O atoms.
> I belive this value will be more reasonably for my purpose. I will
> update the outcome of the result of MD using this restraints after my
> work completes.
> 
> In mean time here is the reference link "
> http://www.jbc.org/cgi/content/full/280/51/42188 "
> 
> For quick find out on the page , use this key work "force constant of 
> 4.0 kcal/mol/Å2" and please let me know the validity of my judgement.
> 
> With Thanks !
> B.Nataraj
> 
> 
> 
> On Wed, 10 May 2006 13:50:17 +0200, "Tsjerk Wassenaar"
> <tsjerkw at gmail.com> said:
> > Hi Raja,
> >
> > No objections from my side. But if you could also include the
> > references resulting from your literature study, that would be nice to
> > have in the archive (may save somebody searching the literature to
> > find some iron - ligand parameters).
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 5/10/06, raja <raja_28 at fastmail.us> wrote:
> > >
> > > Hi gmxions, Based on the litterature search , I am going to use Kb
> > > value of " 4 Kcal/mol A2" (1673.6 KJ/mol nm2)as harmonic bonded
> > > force field constant(type 6) for restraining distance of Fe(II)
> > > ligated with atoms of 2 Nitrogen  and  1 Oxygen. If any one having
> > > objection please correct me ):  .
> > >
> > >
> > > With thanks !
> > > B.Nataraj
> > > --
> > >   raja raja_28 at fastmail.us
> > >
> > > --
> > > http://www.fastmail.fm - Send your email first class
> > >
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> >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and
> > Biotechnology Institute (GBB) Dept. of Biophysical Chemistry
> > University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> -- 
>   raja
>   raja_28 at fastmail.us
> 
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-- 
  raja
  raja_28 at fastmail.us

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