[MMTK] Solvation of the protein hemoglobin

prabhakar g prabha.iisc at googlemail.com
Tue Apr 13 01:05:07 UTC 2010


Hi,

Thank you Dr.Konrad, my study relates to simulation of the protein
hemoglobin and its hydration layer.

But perhaps what you want is to take the protein and crystallographic water
from a PDB file, put it into a larger periodic system, and add lots of
solvent. In that case, the example script to look at is
Examples/MolecularDynamics/
>
> solvation.py.


Yes I tried to solvate a molecule of hemoglobin using the solvate plugin (
http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/)  provided with the
vmd. In case of  hemoglobin there is an inter subunit pocket in between the
four chains of hemoglobin ( stretching approximately to about 10
angstroms).  When i solvate the molecule, this pocket is completely filled
with water molecules.

But when I happen to check with one of the crystal structures (2HHB) of
hemoglobin, this pocket of hemoglobin was sparsely populated with water
molecules.  Sir my question are:

1.Does solvating the structure for simulations place more number of water
molecules  around and in the pocket of the protein molecule than observed in
the physiological conditions.

2.Is it possible to know probability of the  the inter subunit pocket being
completely filled with water molecules in physiological conditions, in
protein solutions.

3. What are the methods could one use to solvate the protein close to the
realistic physiological conditions.

could anyone please give some suggestions.

Sincerely
prabha
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