Hello I did 100 ns simulation using GROMACS a protein protein complex ( chain A for antigen - chain B & C for antibody) now I want to calculate the number of hydrogen bonds. I select chain A and chain B, but it shows nothing. What i should select for selection 1 and selection 2?
Assuming the proteins have unique chain identifiers, A and B:
Selection 1: protein and chain A
Selection 2: protein and chain B
You can also use Gromacs to do it with the command gmx hbond.
Just remember to include an index (-n) with your proteins in two different groups and add -num to get the number of hydrogen bonds as a function of time.
@Magnus Bertelsen.
I also want to calculate %hydrogen occupancy. How I can calculate through gromacs. (I already genrated xpm and index file)
Mohit Kumar
Yeah, I know the %hydrogen occupancy table from the VMD method although I don't know if you can get something similar doing it directly with Gromacs.
Have you tried writing "residue X to Y" in the selection boxes for the VMD method (with X being the first residue of the individual protein and Y the last)?
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