[gmx-users] intrapeptide hbond existence map

[Justin A. Lemkul]

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
> 
> 
> 
> 
> 
> 
> 

-- 
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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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