Dear all,
Using Gromacs, I'm able to record the number of hydrogen bonds between two proteins (no overlap) as a function of time. I am interested though in which particular pair of residues contributes to hydrogen bonding in one time step, and I want to be able to sum these up. By the end of the trajectory I should be able to plot what looks like a matrix made up on pairs of donor-acceptor residues, with the number of hydrogen bonds they "potential" formed as a colour (like a heat map). Is there any ready available software that can do this?
Thanks
Anthony
g_hbond produces this with -hbm (the matrix) and -hbn (to map which atoms are what in the matrix).
Shame on me for missing this - I read the help section over 3 times. Too preoccupied watching Homeland.
Thanks
Anthony
U should use -b and -e flags to specify ur desired time with proper atom indexing. To design a matrix u just have to export the o/p using some editor (e.g. Editplus).
Good luck
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