How do you calculate a hydrogen bond analysis between a residue and DNA in GROMACS?

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Justin Lemkul

Do you want the hydrogen bonds between a specific protein residue and a specific nucleotide? If that's the case, just make each residue its own group and select those two groups when prompted by g_hbond.

Urszula Sylwia Uciechowska-Kaczmarzyk

Yes specific protein residue and specific nucleotide. I am not sure how to specify the nucleotide, if I have DA2 - should I write it r2?

If that's how it is listed in the input file, yes. The 'r' option always takes an integer value or range of values for the desired residue(s). It is simple to check the output to make sure that the atom numbers correspond to the residue(s) you want to analyze.