I used this command to know the salt bridges in my protein
g_saltbr -f md.trr -s md.tpr
but how do I show the graphs and other details for salt bridges with gromacs?
Hi Ibrahim
I will advice you to use VMD to show that. You can import your coordinate file and also the trajectory produced in GROMACS. There is an option in VMD called "timeline" in which you can display in a graphical manner the evolution of several parameters along the simulation, including the salt-bridges.
Best.
Hi Ibrahim
I will advice you to use VMD to show that. You can import your coordinate file and also the trajectory produced in GROMACS. There is an option in VMD called "timeline" in which you can display in a graphical manner the evolution of several parameters along the simulation, including the salt-bridges.
Best.
The g_saltbr program is rather stupid in its approach. It considers anything charged to be a participant in salt bridges, including ions floating around in solution, so the output is cumbersome. Francisco's suggestion is a good one. If you prefer to do things within Gromacs, g_dist with suitable index groups is a much better way to go. Identify important functional groups from the literature or your own observations of the trajectory, make the corresponding groups, and use g_dist to track persistence of interactions.
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