Yes, I am using united atoms. I am looking for H-bonds between phosphate groups of lipids and the H-bonding atoms of the protein. i have used g_hbond to find the relevant intra-protein H-bonds, but need to find protein-lipid H-bonds.
I tried using g_hbond, using the protein and POPC as the two groups, but g_hbond does not detect any acceptor or donor atoms in POPC, because I get something like: ===================== Calculating hydrogen bonds between SideChain_ARG_12 (12 atoms) and POPC (17524 atoms) Found 3 donors and 3 acceptors ===================== So, the question is: where are the listings for acceptor and donor atoms for using g_hbond I hope this clarifies issues. Thank you -Maria On Thu, Apr 17, 2008 at 5:11 PM, <[EMAIL PROTECTED]> wrote: > Are you using united atom lipids? If so, you may want to reconsider > attempting this. If not, you'll be more likely to get further assistance if > you provide quite a bit more information and demonstrate that you invested > some time trying to solve this. > > -- original message -- > > Yes, I looked into that. But could not find any information about how to > include new acceptor or donor atoms. Could you please be more specific ? > Thank you ! > > On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]> > wrote: > > [Hide Quoted Text] > Quoting maria goranovic <[EMAIL PROTECTED]>: > Dear All, > > Where are the donor and acceptor atoms defined for the g_hbond analysis > ? I > was trying to calculate h-bonds between a peptide and a popc bilayer, > but > there are no acceptor or donors listed for POPC. How can one change this > ? > Have a look at g_hbond -h > > -Justin > > Sincerely, > -Maria > > -- > Maria G. > Technical University of Denmark > Copenhagen > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 thewww interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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