[gmx-users] g_hbond results is bus error.

Itamar Kass ikass at cc.huji.ac.il
Sat May 15 22:32:25 CEST 2004

   Hi all, 
    I have a MD simulation of four peptide chains, as part of my analysis I wish
to analys the hydrogen bond change between a residue and its four neighbors.  In
order to do this I try to use  g_hbond.   In order to analysis specific bonds I
built hbond.ndx file:
[ selected ]
   127 128 365
   127 128 368
   127 128 602
   127 128 605
The first atom (127) is the donor (N), the second is the Hydrogen and the third
is the acceptor (O).  The command given was “g_hbond -f system_from_MD.xtc -s
system_for_MD.tpr -num hbond_c_alpha_proton_1.xvg -sel hbond.ndx” and the
machine replayed:
“Reading file system_for_MD.tpr, VERSION 3.2.1 (single precision)
Select group with selected atoms:
Group     0 (    selected) has    12 elements
There is one group in the index
Bus error”.
  The machine is Dual G5 with OSX.3 and we use GROMACS3.2.1, I will appreciate
any help or advice.

p.s. Even when hbond.ndx and the whole system index file was combined, the
results was bus error.

              Thanks you all, Itamar Kass.

Computers are like airconditioners... They don't work well with Windows

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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