Hi everyone. I have a trajectory that was calculated by Gromacs.
1) How can I calculate an h-bond lifetime between two selected amino acids (for example Arg32 (from A chain) and Glu 21 (from B chain))?
2) How can I calculate all h-bonds lifetime between two different protein chains?
Thanks
I am not sure that you will find such tool. I think that you have to write your own analysis code.
Hi Bulat!
You can do that by using the function gmx distance. Then you'll need to provide the index file for that h-bond which you want to study. gmx distance calculates the distance between pairs of particles as the function of time. You can also check gmx pairdist. On the other hand you may write your own code where you analyze trajectory by yourself. It is very easy too.
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