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
Thank you in advance for your help
Stephane
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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