How do I use gmx hbond to find hbonds % occupancy?
I am doing H-bond analyses, and I want to get % h-bond occupancy between a protein and a peptide. I am using the gmx hbond, and I created indices for the protein and for the peptide to analyze hbonds between the two indices. However, none of the output has the donor-acceptor % occupancy.
Any suggestions will be appreciated.
You can not get % occupancy directly from gmx hbond. You can extract the occupancy by analysing the time series of each selected hydrogen bond. To get information you need, the option -hbn -hbm ( gmx hbond) may be useful.
I have a script that does this: https://osf.io/3wunt/
Please make sure to read the instructions in the header carefully; it is a clunky script that I wrote many years ago so it requires some changes to the input files to make everything work.