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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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