[gmx-users] % of existence of hydrogen bond

Erik Marklund erikm at xray.bmc.uu.se
Thu Oct 29 15:47:01 CET 2009


The xpm-file matches the [ hbonds ] index group in the index file spat 
out by g_hbond. X:th line in the map is the h-bond given by the 4:th 
entry in the index group. Be careful when matching the rows though, 
because in the xpm file the first line of data is the bottom row of the 
matrix if I remember correctly.


Moutusi Manna skrev:
> Dear all,
>         I am dealing with a POPC+PEPTDE+WATER system. Basic residues 
> of the peptide make hydrogen bonds with lipid headgroup (as reflected 
> from g_rdf analysis) and the number of hydrogen bonds formed can be 
> calculated from g_hbond program. Now, i want to calculate the % of 
> trajectory time for which a bond between a particular group (say LYS 
> and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving 
> (using xpm2ps) that i got a .eps file, which is a picture file of 
> h_bond existence map, but the data sheet is not given.
> Can any one help me to solve this problem?
> With regards,
> Moutusi Manna
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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

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