Hi Diana, > Well, minorities should not be disregarded just because they are poorly > represented...In some cases a rare event makes all the difference. I think > it would be helpeful to have the possiblity to calculate S-H...X bonds or > X-H...S bonds with g_hbond.
In many cases these tools come about on a per-need-implementation basis. You or any of your colleagues is most welcome to provide a modification of g_hbond that will calculate hydrogen bonds other than O|N-H-O|N. You can't really expect somebody to just invest time to make your life easy, without profit for him/herself. > We found a simple, although, not very elegant way to get around the > question. What we did was to create a topology, for hbond calculation > purposes only, where SG in a given cysteine was replaced by an OG. Basicaly, > we used a sulfur disguised of oxigen, what an atom has to do to be accepted > as one of the guys :P This assumes that the geometrical criteria for hydrogen bonds involving sulfur are equal to those involving oxygen and/or nitrogen. But is that true? Sulfur is much larger and has much more delocalization of charge. This will alter the properties of hydrogen bonds. For instance, the hydrogen bond is much weaker, ergo has a much shallower potential well, and will thus have a broader distribution that might be considered 'hydrogen bond'. On the other hand, the weakness might actually call for a stricter definition. The angle will definitely have a broader range, because of delocalization of electrons over the atomic surface. It's not that easy... But that's just my two cents. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
