[gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond

[Erik Marklund]

There were a few bugfixes done to g_hbond since 4.5.3. Try a more recent version.

Erik


23 okt 2012 kl. 17.41 skrev bipin singh:

> Hello all,
> 
> I was trying to calculate solvent mediated H-bond between a amino acid
> residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after
> creating separate index) with the help of g_hbond version 4.5.3. But I am
> getting segmentation fault while running g_hbond. Moreover I am getting
> error only for this particular residue, whereas with other residues the
> samilar calculation is working fine.
> I have used the following command for the calculation:
> 
> g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log
> -dist hbdist.xvg -hbm hbmap.xvg -n index.ndx
> 
> Please provide your suggestions to rectify the error.
> 
> -- 
> -----------------------
> *Thanks and Regards,*
> Bipin Singh
> -- 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html