[gmx-developers] g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Tue Apr 12 14:48:35 CEST 2011

Nilesh Dhumal skrev 2011-04-12 14.40:
> Hello,
> I am intested in O-H---CL interaction in my system.
> I tried to use contact and -da together with following  command
> g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc   -noda   -r 0.5
> -contact   -num
> I am getting following error.
> Fatal error:Can not analyze contact between H and A: turn off -noda
> Nilesh
So I think that the problem lies in the machinery that identifies donors 
and acceptors. We should allow the combination of arguments that you 
used, but it's more involved than just omitting the agument-combination 
check. Feel free to make a patch for it, or you'll have wait until I, or 
someone else, have a crack at it. I'll put it on my to-do list for 
g_hbond, but there's this thesis defence I have to prepare, so don't 
expect me to implement this over the next few weeks.


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

More information about the gromacs.org_gmx-developers mailing list