Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ?
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