[gmx-users] Re: Re: Regarding umbrella sampling simulations along H-bonds

[neeru sharma]

Dear Stephan Watkins,

Thanks for your response. I would again like to specify my query to my
main concerns. My main query lies for the 2 H-bonds:  one between
Protein and MG and
other one between protein and GTP.

1) I have 2 configurations of my system. In the initial state:
Prot-Mg-GTP complex (Without 2 hbonds ) and final state: Prot-Mg-GTP
complex (With 2 hbonds )
  I was looking, if there is some way to perform umbrella sampling and
then perform WHAM analysis or to calculate PMF for this system, which
would also be based these 2 Hbonds ?

2) Also, I have the trajectory traversing the formation of these
Hbonds during the course of simulation. Can I use this trajectory to
perform some analysis based on these H bonds in terms of free energy,
PMF or energy barrier needed to reach to the final state? But as far
as I understand, gromacs takes electrostatic energy term into
consideration and there is no such specific treatment for H-bonds in
terms of energy calculation.

3) One more thing, can I use pull code in my case where one atom (of
the protein and connected to rest of the protein too) forms a H-bond
with Mg and another atom with GTP ?

4) Or is there any better way to calculate some kind of energy barrier
or PMF needed to form these 2 H-bonds along the simulation length?


Any suggestion is welcome.


Thanks,

Neeru




Dear Neeru Sharma,

I know off hand from years of work with Mg-GTP sites, they are
realativly rigid/staritforward.  If the bonds arn't present with
occupied GTP, or Mg at the beggining, you should equilabrate your
starting structures more.  Unless your looking at the GTP binding to
Mg in which case, the Mg bonds should at least be present.  Mg wont
leave the site under norm conditions, unless the protein is unfolded
(or recycled in cell biological or biochemical terms), or outcompeted
with a higher affine ion.

> Can anyone suggest me what parameters or pull_geometry shall I use, to
> perform the same. Any suggestion is welcome!

Thats too experiment specific to say, without knowing what your trying
to look at.

Grüess

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Thu, 28 Jun 2012 23:30:38 +0530
> Von: neeru sharma <neeru.bioinfo at gmail.com>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Regarding umbrella sampling simulations along H-bonds

> Dear Gromacs Users,
>
> I am simulating a system containing Protein-Mg-GTP complex.
>
> I intend to perform the umbrella sampling on the system to calculate
> PMF and to perform wham analysis.
> I have generated a series of conformations for the umbrella sampling.
> My main consideration is towards the 2 H-bonds: one between Protein
> and MG and other one between protein and GTP. Both of these bonds were
> absent during the start of the simulation but formed when the
> simulation was completed.
>
> Can anyone suggest me what parameters or pull_geometry shall I use, to
> perform the same. Any suggestion is welcome!
>
>
> --
> Thanks and regards,
> Neeru