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. With thanks! B.Nataraj On Thu, 03 Aug 2006 16:12:41 +0200, "David van der Spoel" <[EMAIL PROTECTED]> said: > raja wrote: > > Hi XAvier, > > Thanks again, I meant the resistance caused due to dielectric of water > > separating two charged residues. I doubt whether it will allow the > > transfer of charge between them in order for hydrogen bond to be > > effected. > It's still unclear. > > The hydrogen bonds you find are there because they are apparently > stronger than hbonds with water. However they will still be broken > intermittently. > > -- > 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 - Send your email first class _______________________________________________ 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
