[gmx-users] g_hbond -contact -xpm does not work

Michel Cuendet michel.cuendet at isb-sib.ch
Sun Jan 6 21:00:15 CET 2008


I'm trying to look at contacts between two proteins at the individual 
atom level. I have a bunch of analysis scripts that use the .xpm file 
and work for h-bonds, so I wanted to use the output of g_hbond 3.3.2 
again with the option -contact. But:

g_hbond -hbn -hbm -num -contact -r 0.4

gives the output/error below. The .ndx and .xvg files are created but 
not the .xpm. Apparently there is an interference with the new but 
undocumented option -r2 in the code, involving a confusion between  
hb->nrdist and hb->nrhb... I cannot use earlier versions, because the 
xpm output was very buggy.

The help of g_hbond -h is still version 3.3.1, and the man page is 
version 3.3_beta_20050823. I tend to believe that undocumented options 
are totally useless in a production distribution, and sometimes even 
harmful ;-) I tried to text-mine the mailing list, but couldn't figure 
out exactly what the new g_hbond is supposed to do with -r2 and -contact...

Is there an updated version of g_hbond in the cvs or somewhere ?


Found 1783 different contacts in trajectory
Found 0 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 1783 to 1783
- Reduced number of distances from 0 to 0

Back Off! I just backed up contact.ndx to ./#contact.ndx.2#

Back Off! I just backed up contactnum.xvg to ./#contactnum.xvg.2#
Average number of contacts per timeframe 0.000 out of 2.27314e+06 possible

Program g_hbond, VERSION 3.3.2
Source code file: gmx_hbond.c, line: 2282

Range checking error:
Variable y has value 0. It should have been within [ 0 .. 0 ]


More information about the gromacs.org_gmx-users mailing list