Dear Jason,
First of all thanks a lot.
I read that "It is known that zinc ion binding plays an important role in the stability and dynamics of the zinc finger proteins, which may affect the protein-DNA interactions.To maintain the tetrahedral structures of the
zinc binding sites of the Cys2His2 coordination, the cationic
pseudoatom representation42 was employed instead of a simple nonbonded representation. In the cationic pseudoatom representation, the zinc ion is replaced by a neutral zinc atom centered
at a tetrahedron formed by four massless pseudoatoms with
charge +0.5e. The +2e charge of the zinc ion is restored for
the subsequent MM-PBSA analysis. The zinc ion coordination
geometry obtained in this way was confirmed to be stable around
0.5 Å from the crystal structure throughout the MD simulations
for all of the three zinc binding sites."
From the following article: http://compbio.snu.ac.kr/publications/2010-zinc-finger.pdf
Can this be the solution?
I did calculate the entropy
On Monday, March 17, 2014 6:29 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Mon, 2014-03-17 at 07:58 -0700, Roza M wrote:
> My result for the binding free energy of Zif268-Dna complex was - 206
> kcal/mol
> and delta G value was -111kcal/mol, from this values I calculated kd
> and the result was very far from the experimental values.
MM/PBSA is notoriously bad for computing absolute binding free energies.
You can get decent estimates in some cases, but that requires careful
inclusion of solute entropy effects. (Look for citations from the Ryde
group regarding careful systematic studies of end-state free energy
methods like MM/PBSA).
> I made a pdb files from 1AAY.top and ( min.rst , heat.rst,
> density.rst, equil.rst, prod.rst) and viewed them in pymol to see
> where did I went wrong. I noticed that the zinc ion is moving away
> from its original position each step until finally it went out of the
> protein !!
> Although I used the following restraint each step
> Hold ZNA fixed
> 50.0
> RES 108 110
> END
> END
>
> How can I solve this problem?
Improved parameters, maybe you're missing some bonds... there are many
reasons you could be seeing problems like this. You should carefully
examine the parameters you used and compare them with the parameters
stored in the topology file (you can use ParmEd to do this with the
commands 'printBonds', 'printAngles', 'printDihedrals', etc.). This is
potentially a _very_ difficult problem to diagnose remotely via mailing
list. The key is to figure out exactly what is forcing the zinc out of
the protein -- is it an imaging artifact? electrostatic effects? is it a
result of restraints being put on the system? Designing a strategy to
fix a problem is made increasingly easier with the number of details you
know about the problem in the first place.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 17 2014 - 10:00:03 PDT
