raja wrote:
Thanks spoel,
The g_hbond merely report formation of hydrogen bonds because of two
electronegative atoms come closure to certain distance and angle. The
force field used to simulate is also not capable of modeling hydrogen
bond (Afraid whether I am right). If the h_bond computes the hydrogen
bonds inside the active site there is certainty is there since
dielectric is low inside but in outside will it be right to compute the
hydrogen bonds mere based on distance and angle between the two
electronegative atoms present in bulk solvent. There could be mere
electrostatic interaction. But how we can prove that proton is shared
between those atoms.
Sorry if I am making any mistake at fundamental level.
OK, I see what you mean now. First whether or not there is a HBond is a
matter of taste. One can use a geometric criterion or an energy
criterion to decide that. In molecular modeling the transfer of a proton
is not taken into account explicitly. Sharing a proton does not exist in
reality, in my opinion, however one can have fast shuffling of a proton
between two sites, e.g. in the active site of HIV protease, where there
are two Asp residues, one of which is protonated.
The following references may be helpful:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title = {Hydrogen-bond dynamics for the extended simple point
charge mo
del of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages = {579-587}
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson
and N. Ti
mneanu},
title = {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages = {4393-4398}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title = {Temperature-dependent hydrogen bond geometry in
liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages = 075502
}
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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