maria goranovic wrote:
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
It seems from the first paragraph in g_hbond -h that these are
hard-coded in the source code to the likely protein-only H-bonding groups.
However you should read further, because an alternative solution is
described for you.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
