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. <br>
<br>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:<br><br>=====================<br>Calculating hydrogen bonds between SideChain_ARG_12 (12 atoms) and POPC (17524 atoms)<br>
Found 3 donors and 3 acceptors<br>=====================<br><br>So, the question is: where are the listings for acceptor and donor atoms for using g_hbond<br><br>I hope this clarifies issues. Thank you<br><br>-Maria<br><br>
<br><br><br><br><br><div class="gmail_quote">On Thu, Apr 17, 2008 at 5:11 PM, <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
<br>
-- original message --<br>
<br>
Yes, I looked into that. But could not find any information about how to<br>
include new acceptor or donor atoms. Could you please be more specific ?<br>
Thank you !<br>
<br>
On Thu, Apr 17, 2008 at 12:34 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<br>
[Hide Quoted Text]<br>
Quoting maria goranovic <<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>>:<br>
Dear All,<br>
<br>
Where are the donor and acceptor atoms defined for the g_hbond analysis<br>
? I<br>
was trying to calculate h-bonds between a peptide and a popc bilayer,<br>
but<br>
there are no acceptor or donors listed for POPC. How can one change this<br>
?<br>
Have a look at g_hbond -h<br>
<br>
-Justin<br>
<br>
Sincerely,<br>
-Maria<br>
<br>
--<br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen