Dear Gromacs users, I am trying to analyze hydrogen bonding between a Protein and Drug by g_hbond from .xtc and .tpr and .ndx files. I am getting expected results when the H-bond donor and the hydrogen atom is from protein while the hydrogen bond acceptor atom is in the drug. The results are, however, wrong when I am trying to look for H-bond when the donor and hydrogen atoms are from the drug molecule and acceptor atoms are in the protein. My atom names in the drug molecule sometimes start with N or A, such as NC6 (a carbon), NN6 (a nitrogen), NH61 (a hydrogen) etc. and g_hbond is considering all these atoms as hydrogen bond acceptor. I would appreciate if somebody gives a hint to calculate the correct hydrogen bonds in my system.
Thanks Geeta Kant Ph.D. student, NIMHANS, Bangalore, India
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