[gmx-users] g_hbond results is bus error.

[David]

On Sat, 2004-05-15 at 22:32, Itamar Kass wrote:
>    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:

remove line 1159 (roughly) in the code:

      /* Should this be here ? */
      add_hbond(hb,dd,aa,hh,gr0,gr0,-1,FALSE,bMerge);

I already had some doubt whether the line should be there, but
apparently the answer is no...

> 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
> open.
> ********************************************
> 
> ===========================================
> | 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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