[gmx-users] intrapeptide hbond existence map

[Erik Marklund]

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
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys