Justin A. Lemkul skrev:
ABEL Stephane 175950 wrote:
Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB)
during the aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list
for the 28 INTRHB like this
NH--CO
[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 45
53 60 54
....
to obtain the INTRHB existence map i used the command with gmx4.05
g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f
./XTC/Whole_Traj_53A6Center.xtc -b 400000 -e 500000 -hbn
4_Peptide_53A6_hbonds_400_500ns_index -hbm
4_Peptide_53A6_hbonds_400_500ns_Map
The map show in the x and y axis the time and residue (up to 84). I
have no idea what the figure means. The olot is stored here
http://www.st-abel.com/Hbond_occupency.jpg
I want only to know if, for example, the Hbond_occupency for the
group NH or CO of the residu 1
The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the
donor-acceptor pairs to the plot. Find within that index file a
directive that starts with "hbonds" that corresponds to all of the
H-bonds that were found, and thus plotted. Red indicates the H-bond
exists, white means it doesn't. As for occupancy, you'd probably have
to script that to parse the .xpm file and calculate a percentage of
frames for when the particular H-bond exists, or get lifetimes from
g_hbond.
-Justin
…or to define smaller index groups, e.g. the NH- or CO-group of res 1,
and get the number of hydrogen bonds as function of time from the -num
output (default is hbnum.xvg). You would have to repeat this for all
(reasonable combinations of) hbonding groups that you're interested in,
which can result in maaany g_hbond executions. But if the number of
groups are small, then it's certainly doable. It seems from your plot
though, that scripted processing of the -hbm and -hbn output, as Justin
suggests, is the way to go here. Make sure you're matching the index
file to the xpm file in the right way! I've made mistakes in that area
myself.
Erik
Thank you in advance for your help
Stephane
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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