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

[lloyd riggs]

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
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