Dear Spoel,
Thank for your elaborate answer and references. Some times this forum
serves more than just for gromacs, yes it helps to understand some
basics understanding of physical chemistry. I learned lot of fundamental
concepts of protein modeling in this forum, which I could never
understand by reading a book or journal.
Regards,
B.Nataraj
in
On Thu, 03 Aug 2006 17:29:19 +0200, "David van der Spoel"
<[EMAIL PROTECTED]> said:
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list [email protected]
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
[EMAIL PROTECTED]
--
http://www.fastmail.fm - Access all of your messages and folders
wherever you are
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
