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

[David van der Spoel]

Michel Cuendet wrote:
> 
> Hi,
> 
> 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 ?
> 
> Cheers,
> Michel
> 
> =================================================
> [...]
> Found 1783 different contacts in trajectory
> Found 0 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> 2059/2059
> - Reduced number of hbonds from 1783 to 1783
> - Reduced number of distances from 0 to 0
This might be the problem, maybe you  need a different index file, e.g. 
for water you would take only the oxygens and a distance of 0.35 nm.

> 
> 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 ]
> 
> -------------------------------------------------------
Try different contact distances, it seems there are none.

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se